acedb

ACeDB format is the type of file used for the ACe database - first written to store the information from the sequencing of the nematode worm C.elegans. Each sequence line displays within a 50 character limit.

DNA : "BT006818" atggctgatcagctgaccgaagaacagattgctgaattcaaggaagcctt ctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttg gaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcag gatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccc cgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaag aagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaact aacagatgaagaagtagatgaaatgatcagagaagcagatattgatggag acggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag Peptide : "CALM_HUMAN" ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

aln	See clustal format.
asn1	A subset of ASN.1 format containing entry name, accession number, description and sequence. It is similar to the current ASN.1 output of readseq. There is no consistent number of characters on a sequence line.

seq { id { local id 1 }, descr { title "Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds." }, inst { repr raw, mol dna, length 450, topology linear, seq-data iupacna "atggctgatcagctgaccgaagaacagattgctgaattcaaggaagccttctccctatttg ataaagatggcgatggcaccatcacaacaaaggaacttggaactgtcatgaggtcactgggtcagaacccaacagaag ctgaattgcaggatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccccgaatttttgactatga tggctagaaaaatgaaagatacagatagtgaagaagaaatccgtgaggcattccgagtctttgacaaggatggcaatg gttatatcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaactaacagatgaagaagtagatgaaa tgatcagagaagcagatattgatggagacggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag" } } , seq { id { local id 1 }, descr { title "Calmodulin (CaM)." }, inst { repr raw, mol aa, length 148, topology linear, { seq-data iupacaa "ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNG TIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE EFVQMMTAK" } } ,

clustal

Also known as aln format. The beginning of each entry is denoted by the name of the program for which this format is default - Clustal W. Each aligned sequence is broken up into five blocks of ten characters each and displayed underneath each other. The sequence name is represented at the beginning of each section of sequence. Gaps are denoted by a dash (-).

CLUSTAL W(1.4) multiple sequence alignment CaM2 ATGGCTGATC AGCTGACCGA AGAACAGATT GCTGAATTCA AGGAAGCCTT CaM3 ATGGCTGATC AGCTGACCGA AGAACAGATT GCTGAATTCA AGGAAGCCTT CaM1 ATGGCTGATC AGCTGA---- ---------- -------TCA AGGAAGCCTT CaM2 CTCCCTATTT GATAAAGATG GCGATGGCAC CAAA------ ---------- CaM3 CTCCCTATTT GATAAAGATG GCGATGGCAC CAT------- ---------- CaM1 CTCCCTATTT GATAAAGATG GCGATGGCAC CATCACAACA AAGGAACTTG CaM2 ---CTGTCAT GAGGTCACTG GGTCAGAACC CAACAGAAGC TGAATTGCAG CaM3 ---------- ---------- GGTCAGAACC CAACAGAAGC TGAATTGCAG CaM1 GAACTGTCAT GAGGTCACTG GGTCAGAACC CAACAGAAGC TGAATTGCAG CaM2 GATATGATCA ATGAAGTGGA TGCTGATGGT AATGGCACCA TTGACTTCCC CaM3 GATATGATCA ATGAAGTGGA TGCTGATGGT AATGGCACCA TTGACTTCCC CaM1 GATATGATCA ATGAAGTGGA TGCTGATGGT AATGGCACCA TTGACTTCCC CaM2 CGAATTTTTG ACTATGATGG CTAGAAAAAT GAAAGATACA GATAGTGAAG CaM3 CGAATTTTTG ACTATGATGG CTAGAAAAAT GAAAGATACA GATAGTGAAG CaM1 CGAATTTTTG ACTATGATGG CTAGAAAAAT GAAAGATACA GATAGTGAAG CaM2 AAGAAATCCG TGAGGCATTC CGAGTCTTTG ACAAGGATGG CAATGGTTAT CaM3 AAGAAATCCG TGAGGCATTC CGAGTCTTTG ACAAGGATGG CAATGGTTAT CaM1 AAGAAATCCG TGAGGCATTC CGAGTCTTTG ACAAGGATGG CAATGGTTAT CaM2 ATCAGTGCAG CAGAACTACG TCACGTCATG ACAAACTTAG GAGAAAAACT CaM3 ATCAGTGCAG CAGAACTACG TCACGTCATG ACAAACTTAG GAGAAAAACT CaM1 ATCAGTGCAG CAGAACTACG TCACGTCATG ACAAACTTAG GAGAAAAACT CaM2 AACAGATGAA GAAGTAGATG AAATGATCAG AGAAGCAGAT ATTGATGGAG CaM3 AACAGATGAA GAAGTAGATG AAATGATCAG AGAAGCAGAT ATTGATGGAG CaM1 AACAGATGAA GAAGTAGATG AAATGATCAG AGAAGCAGAT ATTGATGGAG CaM2 ACGGACAAGT CAACTATGAA GAATTCGTAC AGATGATGAC TGCAAAATAG CaM3 ACGGACAAGT CAACTATGAA GAATTCGTAC AGATGATGAC TGCAAAATAG CaM1 ACGGACAAGT CAACTATGAA GAATTCGTAC AGATGATGAC TGCAAAATAG CLUSTAL W(1.4) multiple sequence alignment CaM2 ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD CaM3 ---------- ---------- ---------- ---------- ---------- CaM1 ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD CaM2 MINEVDADGN ---------- ----GTIDFP EFLTMMEAFR VFDKDGNGYI CaM3 --------AD ---------- ----QLTEEQ IAEEIREAFR VFDKDGNGYI CaM1 MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI CaM2 SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK CaM3 SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK CaM1 SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

codata

Codata format includes the indentifier (ENTRY) and accession number of the sequence together with the description line (TITLE). The sequence itself starts after the line beginning SEQUENCE and the end of the sequence is denoted by three soliduses (///) on the line directly below the sequence. Characters in a sequence are numbered in blocks of five up to a maximum line display of 30 across the top and consecutively down the left hand side.

ENTRY BT006818 TITLE Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds., 450 bases ACCESSION BT006818 SEQUENCE 5 10 15 20 25 30 1 a t g g c t g a t c a g c t g a c c g a a g a a c a g a t t 31 g c t g a a t t c a a g g a a g c c t t c t c c c t a t t t 61 g a t a a a g a t g g c g a t g g c a c c a t c a c a a c a 91 a a g g a a c t t g g a a c t g t c a t g a g g t c a c t g 121 g g t c a g a a c c c a a c a g a a g c t g a a t t g c a g 151 g a t a t g a t c a a t g a a g t g g a t g c t g a t g g t 181 a a t g g c a c c a t t g a c t t c c c c g a a t t t t t g 211 a c t a t g a t g g c t a g a a a a a t g a a a g a t a c a 241 g a t a g t g a a g a a g a a a t c c g t g a g g c a t t c 271 c g a g t c t t t g a c a a g g a t g g c a a t g g t t a t 301 a t c a g t g c a g c a g a a c t a c g t c a c g t c a t g 331 a c a a a c t t a g g a g a a a a a c t a a c a g a t g a a 361 g a a g t a g a t g a a a t g a t c a g a g a a g c a g a t 391 a t t g a t g g a g a c g g a c a a g t c a a c t a t g a a 421 g a a t t c g t a c a g a t g a t g a c t g c a a a a t a g /// ENTRY CALM_HUMAN TITLE Calmodulin (CaM)., 148 bases ACCESSION P62158 SEQUENCE 5 10 15 20 25 30 1 A D Q L T E E Q I A E F K E A F S L F D K D G D G T I T T K 31 E L G T V M R S L G Q N P T E A E L Q D M I N E V D A D G N 61 G T I D F P E F L T M M A R K M K D T D S E E E I R E A F R 91 V F D K D G N G Y I S A A E L R H V M T N L G E K L T D E E 121 V D E M I R E A D I D G D G Q V N Y E E F V Q M M T A K ///

dbid	Similar to FASTA format with a greater than (>) sign at the start of the description line. This sign is followed by database   identifier   accession   description. The accession number is optional. This format is input only.

>EMBL BT006818 BT006818 Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds. atggctgatcagctgaccgaagaacagattgctgaattcaaggaagccttctccctattt gataaagatggcgatggcaccatcacaacaaaggaacttggaactgtcatgaggtcactg ggtcagaacccaacagaagctgaattgcaggatatgatcaatgaagtggatgctgatggt aatggcaccattgacttccccgaatttttgactatgatggctagaaaaatgaaagataca gatagtgaagaagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaactaacagatgaa gaagtagatgaaatgatcagagaagcagatattgatggagacggacaagtcaactatgaa >SWISSPROT CALM_HUMAN P62158 Calmodulin (CaM). ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN GTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEEFVQMMTAK

ddbj	This is the same as the GenBank format designed for GenBank entries. It contains all features concerned with the sequence as they would appear in the GenBank or GenPept databases. The end of the entry is denoted by double soliduses (//) on the line immediately after the end of the sequence.

LOCUS BT006818 DEFINITION Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds. ACCESSION BT006818 VERSION BT006818.1 KEYWORDS FLI_CDNA. SOURCE Homo sapiens (human). ORGANISM Homo sapiens (human) Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. BASE COUNT 163 a 76 c 112 g 99 t ORIGIN 1 atggctgatc agctgaccga agaacagatt gctgaattca aggaagcctt ctccctattt 61 gataaagatg gcgatggcac catcacaaca aaggaacttg gaactgtcat gaggtcactg 121 ggtcagaacc caacagaagc tgaattgcag gatatgatca atgaagtgga tgctgatggt 181 aatggcacca ttgacttccc cgaatttttg actatgatgg ctagaaaaat gaaagataca 241 gatagtgaag aagaaatccg tgaggcattc cgagtctttg acaaggatgg caatggttat 301 atcagtgcag cagaactacg tcacgtcatg acaaacttag gagaaaaact aacagatgaa 361 gaagtagatg aaatgatcag agaagcagat attgatggag acggacaagt caactatgaa 421 gaattcgtac agatgatgac tgcaaaatag // LOCUS CALM_HUMAN DEFINITION Calmodulin (CaM). ACCESSION P62158 P02593 P70667 P99014 Q61379 Q61380 KEYWORDS 3D-structure; Acetylation; Calcium-binding; KEYWORDS Direct protein sequencing; Methylation; Phosphorylation; Repeat; KEYWORDS Ubl conjugation. SOURCE Homo sapiens (Human). ORGANISM Homo sapiens (Human) Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. BASE COUNT 11 a 0 c 11 g 12 t 114 others ORIGIN 1 ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN 61 GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE 121 VDEMIREADI DGDGQVNYEE FVQMMTAK //

embl

This is the format of the flatfile EMBL entries. It contains all features concerned with the sequence as they would appear in the EMBL database. Each line is identified with a tag, representing the data it contains. The sequence is represented by the SQ tag and end of the entry is denoted by double soliduses (//) on the line immediately after the end of the sequence.

ID BT006818 standard; DNA; UNC; 450 BP. AC BT006818; SV BT006818.1 DE Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds. KW FLI_CDNA. OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. FH Key Location/Qualifiers FH FT source 1..450 FT /db_xref="taxon:9606" FT /db_xref="RZPD:FLEXo833C0415D0" FT /mol_type="mRNA" FT /note="Vector: pDNR-Dual" FT /organism="Homo sapiens" FT /clone="GH00517X1.0" FT /clone_lib="BD Creator(TM) CDS Library derived from MGC FT collection" FT /lab_host="DH5alpha T1 resistant" FT CDS 1..450 FT /codon_start=1 FT /product="calmodulin 1 (phosphorylase kinase, delta)" FT /protein_id="AAP35464.1" FT /translation="MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPT FT EAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAA FT ELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK" SQ Sequence 450 BP; 163 A; 76 C; 112 G; 99 T; 0 other; atggctgatc agctgaccga agaacagatt gctgaattca aggaagcctt ctccctattt 60 gataaagatg gcgatggcac catcacaaca aaggaacttg gaactgtcat gaggtcactg 120 ggtcagaacc caacagaagc tgaattgcag gatatgatca atgaagtgga tgctgatggt 180 aatggcacca ttgacttccc cgaatttttg actatgatgg ctagaaaaat gaaagataca 240 gatagtgaag aagaaatccg tgaggcattc cgagtctttg acaaggatgg caatggttat 300 atcagtgcag cagaactacg tcacgtcatg acaaacttag gagaaaaact aacagatgaa 360 gaagtagatg aaatgatcag agaagcagat attgatggag acggacaagt caactatgaa 420 gaattcgtac agatgatgac tgcaaaatag 450 //

fasta

The fasta format is the default output for your BioBind software suite. It consists of a greater than (>) sign which denotes the beginning of the entry. This is followed by a description of the sequence on the same line. The line immediately after the description is the sequence. The end of the entry in a multiple sequence file is denoted only by the beginning of a second entry at the > sign.

>BT006818 BT006818.1 Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds. atggctgatcagctgaccgaagaacagattgctgaattcaaggaagccttctccctattt gataaagatggcgatggcaccatcacaacaaaggaacttggaactgtcatgaggtcactg ggtcagaacccaacagaagctgaattgcaggatatgatcaatgaagtggatgctgatggt aatggcaccattgacttccccgaatttttgactatgatggctagaaaaatgaaagataca gatagtgaagaagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaactaacagatgaa gaagtagatgaaatgatcagagaagcagatattgatggagacggacaagtcaactatgaa gaattcgtacagatgatgactgcaaaatag >CALM_HUMAN P62158 Calmodulin (CaM). ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN GTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEEFVQMMTAK

fitch

Designed originally for DNA sequences, the Fitch format contains the sequence identifier and the base count on the line immediately preceding the sequence. All bases in the sequence are divided up into blocks of three. There are twenty of these blocks in one line. This format is output format only.

BT006818, 450 bases atg gct gat cag ctg acc gaa gaa cag att gct gaa ttc aag gaa gcc ttc tcc cta ttt gat aaa gat ggc gat ggc acc atc aca aca aag gaa ctt gga act gtc atg agg tca ctg ggt cag aac cca aca gaa gct gaa ttg cag gat atg atc aat gaa gtg gat gct gat ggt aat ggc acc att gac ttc ccc gaa ttt ttg act atg atg gct aga aaa atg aaa gat aca gat agt gaa gaa gaa atc cgt gag gca ttc cga gtc ttt gac aag gat ggc aat ggt tat atc agt gca gca gaa cta cgt cac gtc atg aca aac tta gga gaa aaa cta aca gat gaa gaa gta gat gaa atg atc aga gaa gca gat att gat gga gac gga caa gtc aac tat gaa gaa ttc gta cag atg atg act gca aaa tag

genbank

This format is the same as the flatfiles used in GenBank entries. It contains all features concerned with the sequence as they would appear in the GenBank or GenPept databases. The end of the entry is denoted by double soliduses (//) on the line immediately after the end of the sequence.

LOCUS BT006818 DEFINITION Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds. ACCESSION BT006818 VERSION BT006818.1 KEYWORDS FLI_CDNA. SOURCE Homo sapiens (human). ORGANISM Homo sapiens (human) Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. BASE COUNT 163 a 76 c 112 g 99 t ORIGIN 1 atggctgatc agctgaccga agaacagatt gctgaattca aggaagcctt ctccctattt 61 gataaagatg gcgatggcac catcacaaca aaggaacttg gaactgtcat gaggtcactg 121 ggtcagaacc caacagaagc tgaattgcag gatatgatca atgaagtgga tgctgatggt 181 aatggcacca ttgacttccc cgaatttttg actatgatgg ctagaaaaat gaaagataca 241 gatagtgaag aagaaatccg tgaggcattc cgagtctttg acaaggatgg caatggttat 301 atcagtgcag cagaactacg tcacgtcatg acaaacttag gagaaaaact aacagatgaa 361 gaagtagatg aaatgatcag agaagcagat attgatggag acggacaagt caactatgaa 421 gaattcgtac agatgatgac tgcaaaatag // LOCUS CALM_HUMAN DEFINITION Calmodulin (CaM). ACCESSION P62158 P02593 P70667 P99014 Q61379 Q61380 KEYWORDS 3D-structure; Acetylation; Calcium-binding; KEYWORDS Direct protein sequencing; Methylation; Phosphorylation; Repeat; KEYWORDS Ubl conjugation. SOURCE Homo sapiens (Human). ORGANISM Homo sapiens (Human) Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. BASE COUNT 11 a 0 c 11 g 12 t 114 others ORIGIN 1 ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN 61 GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE 121 VDEMIREADI DGDGQVNYEE FVQMMTAK //

gff

This is the General Feature Format created at the Sanger Institute for Genome data. Each comment line is started with a double hash (##) and it contains the version numbers of the gff format and the program used to create the file, the date of creation and the sequence identifier. Each piece of information is on a separate line. Information follows the format [attributes] [comments] The end of the entry is denoted by the word end and the type of sequence.

##gff-version 2 ##source-version EMBOSS 2.9.0bb280604 ##date 2004-08-28 ##DNA BT006818 ##atggctgatcagctgaccgaagaacagattgctgaattcaaggaagccttctccctattt ##gataaagatggcgatggcaccatcacaacaaaggaacttggaactgtcatgaggtcactg ##ggtcagaacccaacagaagctgaattgcaggatatgatcaatgaagtggatgctgatggt ##aatggcaccattgacttccccgaatttttgactatgatggctagaaaaatgaaagataca ##gatagtgaagaagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat ##atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaactaacagatgaa ##gaagtagatgaaatgatcagagaagcagatattgatggagacggacaagtcaactatgaa ##gaattcgtacagatgatgactgcaaaatag ##end-DNA ##gff-version 2 ##source-version EMBOSS 2.9.0bb280604 ##date 2004-08-28 ##Protein CALM_HUMAN ##ADQLT EEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN ##GTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE ##VDEMIREADIDGDGQVNYEEFVQMMTAK ##end-Protein

gcg

First used as a format for the Genetics Computer Group software written in Wisconsin, USA, it became the format for the Wisconsin Package as a commercial sequence analysis package. The start of the entry is denoted by a double bang (!!) followed by a definition of the sequence type - nucleotide (NA) or protein (AA). The description is on the line immediately below and one line below that, the sequence information as identifier    sequence length   sequence type   checksum. The checksum is a value based on the sequence, and if the sequence is manually altered, the checksum will no longer tally with the sequence and it will be rejected as an input file. This format is used for GCG releases 9.x and 10.x files. The sequence is displayed on each line as five blocks of ten.

!!NA_SEQUENCE 1.0 Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds. BT006818 Length: 450 Type: N Check: 7527 .. 1 atggctgatc agctgaccga agaacagatt gctgaattca aggaagcctt 51 ctccctattt gataaagatg gcgatggcac catcacaaca aaggaacttg 101 gaactgtcat gaggtcactg ggtcagaacc caacagaagc tgaattgcag 151 gatatgatca atgaagtgga tgctgatggt aatggcacca ttgacttccc 201 cgaatttttg actatgatgg ctagaaaaat gaaagataca gatagtgaag 251 aagaaatccg tgaggcattc cgagtctttg acaaggatgg caatggttat 301 atcagtgcag cagaactacg tcacgtcatg acaaacttag gagaaaaact 351 aacagatgaa gaagtagatg aaatgatcag agaagcagat attgatggag 401 acggacaagt caactatgaa gaattcgtac agatgatgac tgcaaaatag !!AA_SEQUENCE 1.0 Calmodulin (CaM). CALM_HUMAN Length: 148 Type: P Check: 2160 .. 1 ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD 51 MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI 101 SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

gcg8	This format has the same origins and requisites of gcg format, but is the format used by GCG release 8.x.

Hennig86

Designed for DNA data, the Hennig86 format translates each base into a number where A = 0; T = 1; G = 2; C =3. The start is denoted by the comment xread and is followed on a separate line by the application and creation date of the file enclosed in single quotes separated from the text by whitespace. A separate line records the sequence length and number of sequence files represented (in this case 1). Immediately below this line is the identifier line and below this the sequence in numerical form. The end of the entry is denoted by a semi-colon (;). The entire sequence is displayed on a single line.

xread ' Written by EMBOSS 28/06/04 ' 450 1 BT006818 012231201302312033200200302011231200113002200233113133310111201000201223201223033013030030002200311220031213012022130312221302003330030200231200112302201012013001200212201231201221001223033011203113333200111112031012012231020000012000201030201021200200200013321202230113320213111203002201223001221101013021230230200310321303213012030003110220200000310030201200200210201200012013020200230201011201220203220300213003101200200113210302012012031230000102 ;

ig

Intelligenetics format was created for the IntelliGenetics software suite and designed for DNA. The start of the entry is denoted by a semi-colon (;) followed by the sequence description and base count. The sequence identifier is on the next line down followed on the next by the sequence. The end of the entry is denoted by the number 1 on the final sequence line. There are 50 bases displayed on each line of sequence.

;Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds., 450 bases BT006818 atggctgatcagctgaccgaagaacagattgctgaattcaaggaagcctt ctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttg gaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcag gatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccc cgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaag aagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaact aacagatgaagaagtagatgaaatgatcagagaagcagatattgatggag acggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag1

jackknifer

Jackknifer format starts with a single quote separated from the application and creation date by a single whitespace. The sequence is displayed on the subsequent lines with the identifier enclosed by parentheses and separated from the block of 50 sequence characters. The end of the entry is denoted by a semi-colon (;) on a separate line.

' Written by EMBOSS 28/06/04 (BT006818) atggctgatcagctgaccgaagaacagattgctgaattcaaggaagcctt (BT006818) ctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttg (BT006818) gaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcag (BT006818) gatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccc (BT006818) cgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaag (BT006818) aagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat (BT006818) atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaact (BT006818) aacagatgaagaagtagatgaaatgatcagagaagcagatattgatggag (BT006818) acggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag ; ' Written by EMBOSS 28/06/04 (CALM_HUMAN) ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD (CALM_HUMAN) MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI (CALM_HUMAN) SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK ;

jackknifernon

Jackkniferon format starts with a single quote separated from the application and creation date by a single whitespace. The sequence identifier is displayed on the subsequent line encased in parentheses and separated from the first block of 50 sequence characters by whitespace. Each subsequent sequence line is displayed underneath. The end of the entry is denoted by a semi-colon (;) on a separate line.

' Written by EMBOSS 28/06/04 (BT006818) atggctgatcagctgaccgaagaacagattgctgaattcaaggaagcctt ctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttg gaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcag gatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccc cgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaag aagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaact aacagatgaagaagtagatgaaatgatcagagaagcagatattgatggag acggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag ; ' Written by EMBOSS 28/06/04 (CALM_HUMAN) ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK ;

mega

This contains the comment line #mega and the application and creation date on the subsequent line. This is separated from the sequence by a blank line. The sequence lines starts with the hash (#) character and the sequence identifier with whitespace before the sequence is displayed as blocks of 50 characters.

#mega TITLE: Written by EMBOSS 28/06/04 #BT006818 atggctgatcagctgaccgaagaacagattgctgaattcaaggaagcctt #BT006818 ctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttg #BT006818 gaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcag #BT006818 gatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccc #BT006818 cgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaag #BT006818 aagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat #BT006818 atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaact #BT006818 aacagatgaagaagtagatgaaatgatcagagaagcagatattgatggag #BT006818 acggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag #mega TITLE: Written by EMBOSS 28/06/04 #CALM_HUMAN ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD #CALM_HUMAN MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI #CALM_HUMAN SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

meganon

This is similar to mega format but there is no break in the sequence line.

#mega TITLE: Written by EMBOSS 28/06/04 #BT006818 atggctgatcagctgaccgaagaacagattgctgaattcaaggaagccttctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttggaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcaggatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccccgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaagaagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttatatcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaactaacagatgaagaagtagatgaaatgatcagagaagcagatattgatggagacggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag #mega TITLE: Written by EMBOSS 28/06/04 #CALM_HUMAN ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

nexus

Nexus interleaved format, also known as PAUP format is the default output for the PAUP suite of phylogeny programs and is designed to represent DNA sequence only. The entry is headed by the #NEXUS comment line followed on the next line by the application and creation date. There is a blank line between this information and the start of the sequence data including the number of sequences (in this case 1), length, datatype and representation on missing bases (n) and gaps (-). Each of these information lines is ended with a semi-colon (;). A further blank line separates this information from the matrix comment. The sequence is represented on the succeeding lines starting with the sequence identifier and a block of 50 bases. The end of the sequence is denoted by a semi-colon (;). There follows a blank line and further comment lines ending with a semi-colon (;).

#NEXUS [TITLE: Written by EMBOSS 28/06/04] begin data; dimensions ntax=1 nchar=450; format interleave datatype=DNA missing=N gap=-; matrix BT006818 atggctgatcagctgaccgaagaacagattgctgaattcaaggaagcctt BT006818 ctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttg BT006818 gaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcag BT006818 gatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccc BT006818 cgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaag BT006818 aagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat BT006818 atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaact BT006818 aacagatgaagaagtagatgaaatgatcagagaagcagatattgatggag BT006818 acggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag ; end; begin assumptions; options deftype=unord; end;

nexusnon

This format is similar to nexus format but the sequence is displayed on a single line with no breaks.

#NEXUS [TITLE: Written by EMBOSS 28/06/04] begin data; dimensions ntax=1 nchar=450; format datatype=DNA missing=N gap=-; matrix BT006818 atggctgatcagctgaccgaagaacagattgctgaattcaaggaagccttctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttggaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcaggatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccccgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaagaagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttatatcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaactaacagatgaagaagtagatgaaatgatcagagaagcagatattgatggagacggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag ; end; begin assumptions; options deftype=unord; end;

ncbi	This is a similar format to the fasta format to contain NCBI specified information. The description line contains the comments gn1 and unk separated by a bar (|) from each other and the sequence description. The sequence begins on the next line.

>gnl|unk|BT006818 (BT006818.1) Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds. atggctgatcagctgaccgaagaacagattgctgaattcaaggaagccttctccctattt gataaagatggcgatggcaccatcacaacaaaggaacttggaactgtcatgaggtcactg ggtcagaacccaacagaagctgaattgcaggatatgatcaatgaagtggatgctgatggt aatggcaccattgacttccccgaatttttgactatgatggctagaaaaatgaaagataca gatagtgaagaagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaactaacagatgaa gaagtagatgaaatgatcagagaagcagatattgatggagacggacaagtcaactatgaa gaattcgtacagatgatgactgcaaaatag >gnl|unk|CALM_HUMAN (P62158) Calmodulin (CaM). ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN GTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEEFVQMMTAK

nbrf	See pir format.

pearson

See fasta format. Use this format if your sequence headers include pipes (|) that you wish to retain.

pfam	See stockholm format.

phylip

This interleaved format is the default format for the PHYLIP suite of phylogeny programs offered with your BioBind software. The entry starts with a sequence (species) count (in this case 3) and the length of the longest sequence. The line immediately below contains the sequence identifier and the first sequence line, with characters displayed in five blocks of ten. The subsequent sequence lines appear justified directly under the first with no identifier. The sequence identifer MUST be a maximum of 10 characters in length but blank spaces and some puntuation marks are acceptable. Those not allowed are parentheses (( )), square brackets ([ ]), colon (:), semi-colon (;) and comma (,). Gap characters are denoted by a dash (-).

3 450 CaM2 ATGGCTGATC AGCTGACCGA AGAACAGATT GCTGAATTCA AGGAAGCCTT CaM3 ATGGCTGATC AGCTGACCGA AGAACAGATT GCTGAATTCA AGGAAGCCTT CaM1 ATGGCTGATC AGCTGA---- ---------- -------TCA AGGAAGCCTT CTCCCTATTT GATAAAGATG GCGATGGCAC CAAA------ ---------- CTCCCTATTT GATAAAGATG GCGATGGCAC CAT------- ---------- CTCCCTATTT GATAAAGATG GCGATGGCAC CATCACAACA AAGGAACTTG ---CTGTCAT GAGGTCACTG GGTCAGAACC CAACAGAAGC TGAATTGCAG ---------- ---------- GGTCAGAACC CAACAGAAGC TGAATTGCAG GAACTGTCAT GAGGTCACTG GGTCAGAACC CAACAGAAGC TGAATTGCAG GATATGATCA ATGAAGTGGA TGCTGATGGT AATGGCACCA TTGACTTCCC GATATGATCA ATGAAGTGGA TGCTGATGGT AATGGCACCA TTGACTTCCC GATATGATCA ATGAAGTGGA TGCTGATGGT AATGGCACCA TTGACTTCCC CGAATTTTTG ACTATGATGG CTAGAAAAAT GAAAGATACA GATAGTGAAG CGAATTTTTG ACTATGATGG CTAGAAAAAT GAAAGATACA GATAGTGAAG CGAATTTTTG ACTATGATGG CTAGAAAAAT GAAAGATACA GATAGTGAAG AAGAAATCCG TGAGGCATTC CGAGTCTTTG ACAAGGATGG CAATGGTTAT AAGAAATCCG TGAGGCATTC CGAGTCTTTG ACAAGGATGG CAATGGTTAT AAGAAATCCG TGAGGCATTC CGAGTCTTTG ACAAGGATGG CAATGGTTAT ATCAGTGCAG CAGAACTACG TCACGTCATG ACAAACTTAG GAGAAAAACT ATCAGTGCAG CAGAACTACG TCACGTCATG ACAAACTTAG GAGAAAAACT ATCAGTGCAG CAGAACTACG TCACGTCATG ACAAACTTAG GAGAAAAACT AACAGATGAA GAAGTAGATG AAATGATCAG AGAAGCAGAT ATTGATGGAG AACAGATGAA GAAGTAGATG AAATGATCAG AGAAGCAGAT ATTGATGGAG AACAGATGAA GAAGTAGATG AAATGATCAG AGAAGCAGAT ATTGATGGAG ACGGACAAGT CAACTATGAA GAATTCGTAC AGATGATGAC TGCAAAATAG ACGGACAAGT CAACTATGAA GAATTCGTAC AGATGATGAC TGCAAAATAG ACGGACAAGT CAACTATGAA GAATTCGTAC AGATGATGAC TGCAAAATAG 3 148 CaM2 ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD CaM3 ---------- ---------- ---------- ---------- ---------- CaM1 ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN ---------- ----GTIDFP EFLTMMEAFR VFDKDGNGYI --------AD ---------- ----QLTEEQ IAEEIREAFR VFDKDGNGYI MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

phylip3

Similar to phylip format, this is the non-interleaved default output of PHYLIP Version 3.2. It includes a YF notation on the initial line.

1 450 YF CaM2 ATGGCTGATC AGCTGACCGA AGAACAGATT GCTGAATTCA AGGAAGCCTT CTCCCTATTT GATAAAGATG GCGATGGCAC CAAA------ ---------- ---CTGTCAT GAGGTCACTG GGTCAGAACC CAACAGAAGC TGAATTGCAG GATATGATCA ATGAAGTGGA TGCTGATGGT AATGGCACCA TTGACTTCCC CGAATTTTTG ACTATGATGG CTAGAAAAAT GAAAGATACA GATAGTGAAG AAGAAATCCG TGAGGCATTC CGAGTCTTTG ACAAGGATGG CAATGGTTAT ATCAGTGCAG CAGAACTACG TCACGTCATG ACAAACTTAG GAGAAAAACT AACAGATGAA GAAGTAGATG AAATGATCAG AGAAGCAGAT ATTGATGGAG ACGGACAAGT CAACTATGAA GAATTCGTAC AGATGATGAC TGCAAAATAG CaM3 ATGGCTGATC AGCTGACCGA AGAACAGATT GCTGAATTCA AGGAAGCCTT CTCCCTATTT GATAAAGATG GCGATGGCAC CAT------- ---------- ---------- ---------- GGTCAGAACC CAACAGAAGC TGAATTGCAG GATATGATCA ATGAAGTGGA TGCTGATGGT AATGGCACCA TTGACTTCCC CGAATTTTTG ACTATGATGG CTAGAAAAAT GAAAGATACA GATAGTGAAG AAGAAATCCG TGAGGCATTC CGAGTCTTTG ACAAGGATGG CAATGGTTAT ATCAGTGCAG CAGAACTACG TCACGTCATG ACAAACTTAG GAGAAAAACT AACAGATGAA GAAGTAGATG AAATGATCAG AGAAGCAGAT ATTGATGGAG ACGGACAAGT CAACTATGAA GAATTCGTAC AGATGATGAC TGCAAAATAG CaM1 ATGGCTGATC AGCTGA---- ---------- -------TCA AGGAAGCCTT CTCCCTATTT GATAAAGATG GCGATGGCAC CATCACAACA AAGGAACTTG GAACTGTCAT GAGGTCACTG GGTCAGAACC CAACAGAAGC TGAATTGCAG GATATGATCA ATGAAGTGGA TGCTGATGGT AATGGCACCA TTGACTTCCC CGAATTTTTG ACTATGATGG CTAGAAAAAT GAAAGATACA GATAGTGAAG AAGAAATCCG TGAGGCATTC CGAGTCTTTG ACAAGGATGG CAATGGTTAT ATCAGTGCAG CAGAACTACG TCACGTCATG ACAAACTTAG GAGAAAAACT AACAGATGAA GAAGTAGATG AAATGATCAG AGAAGCAGAT ATTGATGGAG ACGGACAAGT CAACTATGAA GAATTCGTAC AGATGATGAC TGCAAAATAG 1 148 YF CaM2 ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN ---------- ----GTIDFP EFLTMMEAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK CaM3 ---------- ---------- ---------- ---------- ---------- --------AD ---------- ----QLTEEQ IAEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK CaM1 ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

pir

Also known as nbrf format this entry starts with a greater than (>) sign followed by the type of sequence (D for nucleotide, P for protein, F for fragment) and the number 1 and separated from the sequence identifier by a semi-colon (;). The sequence description is displayed on the next line with the base (character) count separated from the description by a comma (,). The sequence appears on subsequent lines as five blocks of ten characters and the endpoint is denoted by an asterisk (*) immediately after the final sequence character. It is also acceptable to have no whitespace on the sequence lines.

>D1;BT006818 Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, complete cds., 450 bases atggctgatc agctgaccga agaacagatt gctgaattca aggaagcctt ctccctattt gataaagatg gcgatggcac catcacaaca aaggaacttg gaactgtcat gaggtcactg ggtcagaacc caacagaagc tgaattgcag gatatgatca atgaagtgga tgctgatggt aatggcacca ttgacttccc cgaatttttg actatgatgg ctagaaaaat gaaagataca gatagtgaag aagaaatccg tgaggcattc cgagtctttg acaaggatgg caatggttat atcagtgcag cagaactacg tcacgtcatg acaaacttag gagaaaaact aacagatgaa gaagtagatg aaatgatcag agaagcagat attgatggag acggacaagt caactatgaa gaattcgtac agatgatgac tgcaaaatag* >P1;CALM_HUMAN Calmodulin (CaM)., 148 bases ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK*

plain

This format merely holds the sequence as standard text with no formatting at all. As there is nothing to indicate the start or end of a sequence, this type of format is only suitable for single sequence files.

atggctgatcagctgaccgaagaacagattgctgaattcaaggaagcctt ctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttg gaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcag gatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccc cgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaag aagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaact aacagatgaagaagtagatgaaatgatcagagaagcagatattgatggag acggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

raw	See plain format.

selex

Selex is an interleaved multiple alignment format. Machine comment lines at the head of the file are denoted with a hash equals sign (#=). User comment lines can start with either a hash (#) or a percent (%) sign. The #=SQ denotes a comment for each sequence. This must be in the same order the sequences appear. The comment seqeunce is followed by the sequence name,   weight,   database source name,   database accession,   source coordinates (start - stop:original length),  description. Any information not available may be replaced with a dash (-) with the exception of the source coordinates which should contain the number zero (0). Each sequence line contains a name which can be any length, but must include no whitespace. followed by a block of 50 sequence characters. Gaps may be denoted by a dash (-), a dot (.), a blank space or an underscore (_). Sequence characters are case sensitive.

#=SQ CaM2 0.10 - - 0..0:0 - #=SQ CaM3 33.30 - - 0..0:0 - #=SQ CaM1 66.60 - - 0..0:0 - CaM2 ATGGCTGATCAGCTGACCGAAGAACAGATTGCTGAATTCAAGGAAGCCTT CaM3 ATGGCTGATCAGCTGACCGAAGAACAGATTGCTGAATTCAAGGAAGCCTT CaM1 ATGGCTGATCAGCTGA---------------------TCAAGGAAGCCTT CaM2 CTCCCTATTTGATAAAGATGGCGATGGCACCAAA---------------- CaM3 CTCCCTATTTGATAAAGATGGCGATGGCACCAT----------------- CaM1 CTCCCTATTTGATAAAGATGGCGATGGCACCATCACAACAAAGGAACTTG CaM2 ---CTGTCATGAGGTCACTGGGTCAGAACCCAACAGAAGCTGAATTGCAG CaM3 --------------------GGTCAGAACCCAACAGAAGCTGAATTGCAG CaM1 GAACTGTCATGAGGTCACTGGGTCAGAACCCAACAGAAGCTGAATTGCAG CaM2 GATATGATCAATGAAGTGGATGCTGATGGTAATGGCACCATTGACTTCCC CaM3 GATATGATCAATGAAGTGGATGCTGATGGTAATGGCACCATTGACTTCCC CaM1 GATATGATCAATGAAGTGGATGCTGATGGTAATGGCACCATTGACTTCCC CaM2 CGAATTTTTGACTATGATGGCTAGAAAAATGAAAGATACAGATAGTGAAG CaM3 CGAATTTTTGACTATGATGGCTAGAAAAATGAAAGATACAGATAGTGAAG CaM1 CGAATTTTTGACTATGATGGCTAGAAAAATGAAAGATACAGATAGTGAAG CaM2 AAGAAATCCGTGAGGCATTCCGAGTCTTTGACAAGGATGGCAATGGTTAT CaM3 AAGAAATCCGTGAGGCATTCCGAGTCTTTGACAAGGATGGCAATGGTTAT CaM1 AAGAAATCCGTGAGGCATTCCGAGTCTTTGACAAGGATGGCAATGGTTAT CaM2 ATCAGTGCAGCAGAACTACGTCACGTCATGACAAACTTAGGAGAAAAACT CaM3 ATCAGTGCAGCAGAACTACGTCACGTCATGACAAACTTAGGAGAAAAACT CaM1 ATCAGTGCAGCAGAACTACGTCACGTCATGACAAACTTAGGAGAAAAACT CaM2 AACAGATGAAGAAGTAGATGAAATGATCAGAGAAGCAGATATTGATGGAG CaM3 AACAGATGAAGAAGTAGATGAAATGATCAGAGAAGCAGATATTGATGGAG CaM1 AACAGATGAAGAAGTAGATGAAATGATCAGAGAAGCAGATATTGATGGAG CaM2 ACGGACAAGTCAACTATGAAGAATTCGTACAGATGATGACTGCAAAATAG CaM3 ACGGACAAGTCAACTATGAAGAATTCGTACAGATGATGACTGCAAAATAG CaM1 ACGGACAAGTCAACTATGAAGAATTCGTACAGATGATGACTGCAAAATAG #=SQ CaM2 100.00 - - 0..0:0 - #=SQ CaM3 100.00 - - 0..0:0 - #=SQ CaM1 0.10 - - 0..0:0 - CaM2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD CaM3 -------------------------------------------------- CaM1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD CaM2 MINEVDADGN--------------GTIDFPEFLTMMEAFRVFDKDGNGYI CaM3 --------AD--------------QLTEEQIAEEIREAFRVFDKDGNGYI CaM1 MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI CaM2 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK CaM3 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK CaM1 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

staden

This is very similar to plain format with the exception that the sequence is preceded by the sequence name followed by four dashes (-) and encased in angular brackets (< >). There is is no limit to the length of the name, but it must not contain whitespace. Punctuation is also allowed. This sequence name will not be seen on webpages as it is enclosed in angular brackets. Comments may i#be inserted into lines between the naem and the sequencce by preceding them with a semi-colon (;) It was created for the STADEN sequencing software package, although this package generally uses the EMBL format now.

<BT006818----> atggctgatcagctgaccgaagaacagattgctgaattcaaggaagccttctccctattt gataaagatggcgatggcaccatcacaacaaaggaacttggaactgtcatgaggtcactg ggtcagaacccaacagaagctgaattgcaggatatgatcaatgaagtggatgctgatggt aatggcaccattgacttccccgaatttttgactatgatggctagaaaaatgaaagataca gatagtgaagaagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaactaacagatgaa gaagtagatgaaatgatcagagaagcagatattgatggagacggacaagtcaactatgaa gaattcgtacagatgatgactgcaaaatag <CALM_HUMAN----> ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN GTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEEFVQMMTAK

stockholm

This format is used principally in HMMER, Pfam and Belvu as a format for protein sequence. It starts with a hash (#) character followed by the name of the format and a version number (currently 1.0). The aligned sequences can be displayed as a wrap around alignment or with no breaks. The length is optional, but the name is mandatory. The end of the entry is denoted by double soliduses (//) on the line directly after the sequence lines. Gaps are denoted as a dash (-) or a dot (.). This alignment may be annotated using the tags: #=GF  Free text file annotation. Should appear above the alignment. #=GC  Column annotation - only 1 character per column. Should appear below the alignment. #=GS  Free text sequence annotation. Should appear above the alignment or just below corresponding sequence. #=GR  Sequence and column annotation - only one character per column. Should appear just below the corresponding sequence.

# STOCKHOLM 1.0 #=GS CaM2 WT 100.00 #=GS CaM3 WT 100.00 #=GS CaM1 WT 0.10 CaM2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD CaM3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CaM1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD CaM2 MINEVDADGN..............GTIDFPEFLTMMEAFRVFDKDGNGYI CaM3 ~~~~~~~~AD..............QLTEEQIAEEIREAFRVFDKDGNGYI CaM1 MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI CaM2 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK CaM3 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK CaM1 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK //

strider

DNA strider is a simple sequence analysis program designed to run on Mackintosh platforms. The sequence format begins with a comment line denoted by a hash (#) character and the name of the application. Each line above the sequence is denoted by a semi-colon (;). The second line contains the sequence notation,   accession number,   length. A blank line separates this information from the sequence which is displayed as line blocks of fifty bases. The end of the entry is denoted by a double solidus (//) on the line immediately after the last sequence line.

; ### from DNA Strider ;-) ; DNA sequence BT006818, 450 bases ; atggctgatcagctgaccgaagaacagattgctgaattcaaggaagcctt ctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttg gaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcag gatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccc cgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaag aagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttat atcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaact aacagatgaagaagtagatgaaatgatcagagaagcagatattgatggag acggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag //

swissprot

This is the format of the flatfile Swiss-Prot entries. It contains all features concerned with the sequence as they would appear in the Swiss_Prot database. Each line is identified with a tag, representing the data it contains. The sequence is represented by the SQ tag and end of the entry is denoted by double soliduses (//) on the line immediately after the end of the sequence.

ID CALM_HUMAN STANDARD; PRT; 148 AA. AC P62158; P02593; P70667; P99014; Q61379; Q61380; DE Calmodulin (CaM). OS Homo sapiens (Human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. KW 3D-structure; Acetylation; Calcium-binding; Direct protein sequencing; KW Methylation; Phosphorylation; Repeat; Ubl conjugation. SQ SEQUENCE 148 AA; 16707 MW; 464B8A287475A1CA CRC64; ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK //

text	See plain format.
treecon	A very simple format with the length of the sequence displayed at the top of the entry, followed by the sequence identifier on the next line down. The sequence line is immediately below this with no line breaks.

450 BT006818 atggctgatcagctgaccgaagaacagattgctgaattcaaggaagccttctccctatttgataaagatggcgatggcaccatcacaacaaaggaacttggaactgtcatgaggtcactgggtcagaacccaacagaagctgaattgcaggatatgatcaatgaagtggatgctgatggtaatggcaccattgacttccccgaatttttgactatgatggctagaaaaatgaaagatacagatagtgaagaagaaatccgtgaggcattccgagtctttgacaaggatggcaatggttatatcagtgcagcagaactacgtcacgtcatgacaaacttaggagaaaaactaacagatgaagaagtagatgaaatgatcagagaagcagatattgatggagacggacaagtcaactatgaagaattcgtacagatgatgactgcaaaatag 148 CALM_HUMAN ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

debug

This is a verbose format designed for use as a debugging tool. EMBOSS definition tags are listed in alphabetical order and the information contained in the input file written out.

Name: 'BT006818' Accession: 'BT006818' Acclist: (1) BT006818 SeqVersion: 'BT006818.1' GI Version: '' Description: 'Homo sapiens calmodulin 1 (phosphorylase kinase, delta) mRNA, co mplete cds.' Keywordlist: (1) 'FLI_CDNA' Taxonomy: 'Homo sapiens (human)' Taxlist: (13) 'Homo sapiens (human)' 'Eukaryota' 'Metazoa' 'Chordata' 'Craniata' 'Vertebrata' 'Euteleostomi' 'Mammalia' 'Eutheria' 'Primates' 'Catarrhini' 'Hominidae' 'Homo' Type: 'N' Database: 'embl' Full name: '' Date: '' Usa: 'bt006818.debug' Ufo: '' Input format: 'embl' Output format: 'debug' Filename: 'bt006818.debug' Directory: '' Entryname: 'BT006818' File name: 'bt006818.debug' Extension: 'debug' Single: 'No' Features: 'No' Count: 'No' Documentation:... 1 atggctgatc agctgaccga agaacagatt gctgaattca aggaagcctt 50 51 ctccctattt gataaagatg gcgatggcac catcacaaca aaggaacttg 100 101 gaactgtcat gaggtcactg ggtcagaacc caacagaagc tgaattgcag 150 151 gatatgatca atgaagtgga tgctgatggt aatggcacca ttgacttccc 200 201 cgaatttttg actatgatgg ctagaaaaat gaaagataca gatagtgaag 250 251 aagaaatccg tgaggcattc cgagtctttg acaaggatgg caatggttat 300 301 atcagtgcag cagaactacg tcacgtcatg acaaacttag gagaaaaact 350 351 aacagatgaa gaagtagatg aaatgatcag agaagcagat attgatggag 400 401 acggacaagt caactatgaa gaattcgtac agatgatgac tgcaaaatag 450

Alignment Formats EMBOSS currently reads and writes 13 separate alignment formats. This breaks down into 8 different pairwise and 5 different alignment formats. Each alignment output contains a header detailing information on the alignment and the end of entry is denoted by #--------------------------------------- #--------------------------------------- .

Pairwise Alignment Formats

pair

This is the default output for the pairwise alignment modules in your BioBind software. Each sequence is preceded by a name of upto 10 characters long. Numbering is at the ends of each seqeunce line and corresponds to the sequence numbering - thus ignoring gap characters (-). Identical matches are denoted with a bar (|) and similar matches with a colon (:).

CaM1 12 GCTGA--TCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCAC 59 ||||| ||||||||||||||||||||||||||||||||||||||||||| CaM2 31 GCTGAATTCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCAC 80 CaM1 60 CATCACAACAAAGGAACTTGGAACTGTCATGAGGTCACTGGGTCAGAACC 109 || ||||||||||||||||||||||||||||| CaM2 81 CA-------------------AACTGTCATGAGGTCACTGGGTCAGAACC 111 CaM1 110 CAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT 159 |||||||||||||||||||||||||||||||||||||||||||||||||| CaM2 112 CAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT 161 CaM1 160 AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAAT 209 |||||||||||||||||||||||||||||||||||||||||||||||||| CaM2 162 AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAAT 211 CaM1 210 GAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTG 259 |||||||||||||||||||||||||||||||||||||||||||||||||| CaM2 212 GAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTG 261 CaM1 260 ACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATG 309 |||||||||||||||||||||||||||||||||||||||||||||||||| CaM2 262 ACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATG 311 CaM1 310 ACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAG 359 |||||||||||||||||||||||||||||||||||||||||||||||||| CaM2 312 ACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAG 361 CaM1 360 AGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTAC 409 |||||||||||||||||||||||||||||||||||||||||||||||||| CaM2 362 AGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTAC 411 CaM1 410 AGATGATGACTGCAAAATAG 429 |||||||||||||||||||| CaM2 412 AGATGATGACTGCAAAATAG 431 CaM1 1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD 50 |||||||||||||||||||||||||||||||||||||||||||||||||| CaM2 1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD 50 CaM1 51 MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI 100 ||||||||||||||||::|||| |||||||||||||| CaM2 51 MINEVDADGNGTIDFPDYLTMM--------------EAFRVFDKDGNGYI 86 CaM1 101 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148 ||||||||||||||||||||||||||||||||||||||::|||||||| CaM2 87 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYDDFVQMMTAK 134

markx0

Each sequence line is represented with the sequence name as a maximum of six characters separated from the sequence by a whitespace. The markup line is between the sequence lines. An identical match is denoted by a colon (:), a similar match by a dot (.) and a gap by a dash (-). The sequences are numbered in blocks of ten, although the numbering will not necessarily start at 1 depending on where the sequences align. Sequence lines are displayed as blocks of 50 characters.

10 20 CaM1 ATGGCTGATCAGCTGA---------------------TCAAGGAAGCCTT :::::::::::::::: ::::::::::::: CaM2 ATGGCTGATCAGCTGACCGAAGAACAGATTGCTGAATTCAAGGAAGCCTT 10 20 30 40 50 30 40 50 60 70 CaM1 CTCCCTATTTGATAAAGATGGCGATGGCACCATCACAACAAAGGAACTTG :::::::::::::::::::::::::::::::: CaM2 CTCCCTATTTGATAAAGATGGCGATGGCACCA------------------ 60 70 80 80 90 100 110 120 CaM1 GAACTGTCATGAGGTCACTGGGTCAGAACCCAACAGAAGCTGAATTGCAG ::::::::::::::::::::::::::::::::::::::::::::::::: CaM2 -AACTGTCATGAGGTCACTGGGTCAGAACCCAACAGAAGCTGAATTGCAG 90 100 110 120 130 130 140 150 160 170 CaM1 GATATGATCAATGAAGTGGATGCTGATGGTAATGGCACCATTGACTTCCC :::::::::::::::::::::::::::::::::::::::::::::::::: CaM2 GATATGATCAATGAAGTGGATGCTGATGGTAATGGCACCATTGACTTCCC 140 150 160 170 180 180 190 200 210 220 CaM1 CGAATTTTTGACTATGATGGCTAGAAAAATGAAAGATACAGATAGTGAAG :::::::::::::::::::::::::::::::::::::::::::::::::: CaM2 CGAATTTTTGACTATGATGGCTAGAAAAATGAAAGATACAGATAGTGAAG 190 200 210 220 230 230 240 250 260 270 CaM1 AAGAAATCCGTGAGGCATTCCGAGTCTTTGACAAGGATGGCAATGGTTAT :::::::::::::::::::::::::::::::::::::::::::::::::: CaM2 AAGAAATCCGTGAGGCATTCCGAGTCTTTGACAAGGATGGCAATGGTTAT 240 250 260 270 280 280 290 300 310 320 CaM1 ATCAGTGCAGCAGAACTACGTCACGTCATGACAAACTTAGGAGAAAAACT :::::::::::::::::::::::::::::::::::::::::::::::::: CaM2 ATCAGTGCAGCAGAACTACGTCACGTCATGACAAACTTAGGAGAAAAACT 290 300 310 320 330 330 340 350 360 370 CaM1 AACAGATGAAGAAGTAGATGAAATGATCAGAGAAGCAGATATTGATGGAG :::::::::::::::::::::::::::::::::::::::::::::::::: CaM2 AACAGATGAAGAAGTAGATGAAATGATCAGAGAAGCAGATATTGATGGAG 340 350 360 370 380 380 390 400 410 420 CaM1 ACGGACAAGTCAACTATGAAGAATTCGTACAGATGATGACTGCAAAATAG :::::::::::::::::::::::::::::::::::::::::::::::::: CaM2 ACGGACAAGTCAACTATGAAGAATTCGTACAGATGATGACTGCAAAATAG 390 400 410 420 430 10 20 30 40 50 CaM1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD :::::::::::::::::::::::::::::::::::::::::::::::::: CaM2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD 10 20 30 40 50 60 70 80 90 100 CaM1 MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI ::::::::::::::::..:::: :::::::::::::: CaM2 MINEVDADGNGTIDFPDYLTMM--------------EAFRVFDKDGNGYI 60 70 80 110 120 130 140 CaM1 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK ::::::::::::::::::::::::::::::::::::::..:::::::: CaM2 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYDDFVQMMTAK 90 100 110 120 130

markx1

Similar to the markx0 format, with a mark up line that only reports similar matches (x).

20 30 40 50 CaM1 GCTGA--TCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCAC CaM2 GCTGAATTCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCAC 40 50 60 70 80 60 70 80 90 100 CaM1 CATCACAACAAAGGAACTTGGAACTGTCATGAGGTCACTGGGTCAGAACC CaM2 CA-------------------AACTGTCATGAGGTCACTGGGTCAGAACC 90 100 110 110 120 130 140 150 CaM1 CAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT CaM2 CAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT 120 130 140 150 160 160 170 180 190 200 CaM1 AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAAT CaM2 AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAAT 170 180 190 200 210 210 220 230 240 250 CaM1 GAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTG CaM2 GAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTG 220 230 240 250 260 260 270 280 290 300 CaM1 ACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATG CaM2 ACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATG 270 280 290 300 310 310 320 330 340 350 CaM1 ACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAG CaM2 ACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAG 320 330 340 350 360 360 370 380 390 400 CaM1 AGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTAC CaM2 AGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTAC 370 380 390 400 410 410 420 CaM1 AGATGATGACTGCAAAATAG CaM2 AGATGATGACTGCAAAATAG 420 430 10 20 30 40 50 CaM1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD CaM2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD 10 20 30 40 50 60 70 80 90 100 CaM1 MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI xx CaM2 MINEVDADGNGTIDFPDYLTMM--------------EAFRVFDKDGNGYI 60 70 80 110 120 130 140 CaM1 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK xx CaM2 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYDDFVQMMTAK 90 100 110 120 130

markx2

Similar to the markx0 format, but only non-identical matches are shown in the second sequence.

CaM1 GCTGA--TCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCAC CaM2 .....AT........................................... 60 70 80 90 100 CaM1 CATCACAACAAAGGAACTTGGAACTGTCATGAGGTCACTGGGTCAGAACC CaM2 ..-------------------............................. 110 120 130 140 150 CaM1 CAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT CaM2 .................................................. 160 170 180 190 200 CaM1 AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAAT CaM2 .................................................. 210 220 230 240 250 CaM1 GAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTG CaM2 .................................................. 260 270 280 290 300 CaM1 ACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATG CaM2 .................................................. 310 320 330 340 350 CaM1 ACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAG CaM2 .................................................. 360 370 380 390 400 CaM1 AGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTAC CaM2 .................................................. 410 420 CaM1 AGATGATGACTGCAAAATAG CaM2 .................... 10 20 30 40 50 CaM1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD CaM2 .................................................. 60 70 80 90 100 CaM1 MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI CaM2 ................DY....--------------.............. 110 120 130 140 CaM1 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK CaM2 ......................................DD........

markx3

This provides the aligned sequences in fasta format, with a double dot (..) notation after the sequence name on the line directly above the sequence. Characters are displayed in blocks of 50 with gaps denoted by a dash (-) character.

>CaM1 .. GCTGA--TCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCAC CATCACAACAAAGGAACTTGGAACTGTCATGAGGTCACTGGGTCAGAACC CAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAAT GAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTG ACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATG ACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAG AGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTAC AGATGATGACTGCAAAATAG >CaM2 .. GCTGAATTCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCAC CA-------------------AACTGTCATGAGGTCACTGGGTCAGAACC CAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAAT GAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTG ACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATG ACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAG AGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTAC AGATGATGACTGCAAAATAG >CaM1 .. ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK >CaM2 .. ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD MINEVDADGNGTIDFPDYLTMM--------------EAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYDDFVQMMTAK

markx10

Markx10 format is annotation markx3 format. Annotation lines start with a semi-colon (;) and the start, end and length of the alignment.

>CaM1 .. ; sq_len: 420 ; al_start: 1 ; al_stop: 420 ; al_display_start: 1 GCTGA--TCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCAC CATCACAACAAAGGAACTTGGAACTGTCATGAGGTCACTGGGTCAGAACC CAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAAT GAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTG ACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATG ACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAG AGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTAC AGATGATGACTGCAAAATAG >CaM2 .. ; sq_len: 420 ; al_start: 1 ; al_stop: 420 ; al_display_start: 1 GCTGAATTCAAGGAAGCCTTCTCCCTATTTGATAAAGATGGCGATGGCAC CA-------------------AACTGTCATGAGGTCACTGGGTCAGAACC CAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAAT GAAAGATACAGATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTG ACAAGGATGGCAATGGTTATATCAGTGCAGCAGAACTACGTCACGTCATG ACAAACTTAGGAGAAAAACTAACAGATGAAGAAGTAGATGAAATGATCAG AGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAAGAATTCGTAC AGATGATGACTGCAAAATAG >CaM1 .. ; sq_len: 148 ; al_start: 1 ; al_stop: 148 ; al_display_start: 1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK >CaM2 .. ; sq_len: 148 ; al_start: 1 ; al_stop: 148 ; al_display_start: 1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD MINEVDADGNGTIDFPDYLTMM--------------EAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYDDFVQMMTAK

score

This contains no header and displays the two sequence name, sequence length, (score). The score is dependent on the scoring matrix used with the alignment algorithm.

CaM1 CaM2 420 (1887) CaM1 CaM2 148 (607)

srspair

See pair format.

Multiple Alignment Formats There are currently two multiple alignment formats incorporated into your BioBind software suite. The default setting is the fasta format.

fasta

Multiple alignment form of the fasta and default output format. Gaps are denoted by a dash character (-). This type of output is best viewed in your Jemboss Alignment Editor.

>CaM2 ATGGCTGATCAGCTGACCGAAGAACAGATTGCTGAATTCAAGGAAGCCTTCTCCCTATTT GATAAAGATGGCGATGGCACCAAA-------------------CTGTCATGAGGTCACTG GGTCAGAACCCAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAATGAAAGATACA GATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTGACAAGGATGGCAATGGTTAT ATCAGTGCAGCAGAACTACGTCACGTCATGACAAACTTAGGAGAAAAACTAACAGATGAA GAAGTAGATGAAATGATCAGAGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAA GAATTCGTACAGATGATGACTGCAAAATAG >CaM3 ATGGCTGATCAGCTGACCGAAGAACAGATTGCTGAATTCAAGGAAGCCTTCTCCCTATTT GATAAAGATGGCGATGGCACCAT------------------------------------- GGTCAGAACCCAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAATGAAAGATACA GATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTGACAAGGATGGCAATGGTTAT ATCAGTGCAGCAGAACTACGTCACGTCATGACAAACTTAGGAGAAAAACTAACAGATGAA GAAGTAGATGAAATGATCAGAGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAA GAATTCGTACAGATGATGACTGCAAAATAG >CaM1 ATGGCTGATCAGCTGA---------------------TCAAGGAAGCCTTCTCCCTATTT GATAAAGATGGCGATGGCACCATCACAACAAAGGAACTTGGAACTGTCATGAGGTCACTG GGTCAGAACCCAACAGAAGCTGAATTGCAGGATATGATCAATGAAGTGGATGCTGATGGT AATGGCACCATTGACTTCCCCGAATTTTTGACTATGATGGCTAGAAAAATGAAAGATACA GATAGTGAAGAAGAAATCCGTGAGGCATTCCGAGTCTTTGACAAGGATGGCAATGGTTAT ATCAGTGCAGCAGAACTACGTCACGTCATGACAAACTTAGGAGAAAAACTAACAGATGAA GAAGTAGATGAAATGATCAGAGAAGCAGATATTGATGGAGACGGACAAGTCAACTATGAA GAATTCGTACAGATGATGACTGCAAAATAG >CaM2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN --------------GTIDFPEFLTMMEAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEEFVQMMTAK >CaM3 ----------------------------------------------------------AD --------------QLTEEQIAEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEEFVQMMTAK >CaM1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN GTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEEFVQMMTAK

msf

Originally designed as multiple alignment format, the initial information is similar to gcg format. The start of the entry is denoted by a double bang (!!) followed by a definition of the sequence type - nucleotide (NA) or protein (AA). The description of the multiple file format is on the line immediately below with the sequence length, sequence type, creation date and a checksum relating to the alignment. The next line contains the identifiers of each sequence in the alignment followed by their length, and a checksum based on that particular sequence only. Names may contain up to 14 characters and no blank spaces. Lengths must be equal. Gaps are denoted by a tilda (~). This information is separated from the alignment by double soliduses (//) marks. The checksum is a value based on the sequence, and if the sequence is manually altered, the checksum will no longer tally with the sequence and it will be rejected as an input file. The sequence is displayed on each line as a block of fifty and aligned sequences are directly under one another.

!!NA_MULTIPLE_ALIGNMENT 1.0 MSF: 431 Type: N 28/08/04 CompCheck: 2996 .. Name: CaM1 Len: 431 Check: 2743 Weight: 1.00 Name: CaM2 Len: 431 Check: 8399 Weight: 1.00 Name: CaM3 Len: 431 Check: 1854 Weight: 1.00 // 1 50 CaM1 atggctgatcagctgatcaaggaagccttctccctatttgataaagatgg CaM2 atggctgatcagctgaccgaagaacagattgctgaattcaaggaagcctt CaM3 atggctgatcagctgaccgaagaacagattgctgaattcaaggaagcctt 51 100 CaM1 cgatggcaccatcacaacaaaggaacttggaactgtcatgaggtcactgg CaM2 ctccctatttgataaagatggcgatggcaccaaactgtcatgaggtcact CaM3 ctccctatttgataaagatggcgatggcaccatggtcagaacccaacaga 101 150 CaM1 gtcagaacccaacagaagctgaattgcaggatatgatcaatgaagtggat CaM2 gggtcagaacccaacagaagctgaattgcaggatatgatcaatgaagtgg CaM3 agctgaattgcaggatatgatcaatgaagtggatgctgatggtaatggca 151 200 CaM1 gctgatggtaatggcaccattgacttccccgaatttttgactatgatggc CaM2 atgctgatggtaatggcaccattgacttccccgaatttttgactatgatg CaM3 ccattgacttccccgaatttttgactatgatggctagaaaaatgaaagat 201 250 CaM1 tagaaaaatgaaagatacagatagtgaagaagaaatccgtgaggcattcc CaM2 gctagaaaaatgaaagatacagatagtgaagaagaaatccgtgaggcatt CaM3 acagatagtgaagaagaaatccgtgaggcattccgagtctttgacaagga 251 300 CaM1 gagtctttgacaaggatggcaatggttatatcagtgcagcagaactacgt CaM2 ccgagtctttgacaaggatggcaatggttatatcagtgcagcagaactac CaM3 tggcaatggttatatcagtgcagcagaactacgtcacgtcatgacaaact 301 350 CaM1 cacgtcatgacaaacttaggagaaaaactaacagatgaagaagtagatga CaM2 gtcacgtcatgacaaacttaggagaaaaactaacagatgaagaagtagat CaM3 taggagaaaaactaacagatgaagaagtagatgaaatgatcagagaagca 351 400 CaM1 aatgatcagagaagcagatattgatggagacggacaagtcaactatgaag CaM2 gaaatgatcagagaagcagatattgatggagacggacaagtcaactatga CaM3 gatattgatggagacggacaagtcaactatgaagaattcgtacagatgat 401 431 CaM1 aattcgtacagatgatgactgcaaaatag~~ CaM2 agaattcgtacagatgatgactgcaaaatag CaM3 gactgcaaaatag~~~~~~~~~~~~~~~~~~ !!AA_MULTIPLE_ALIGNMENT 1.0 MSF: 148 Type: P 28/08/04 CompCheck: 9511 .. Name: CaM1 Len: 148 Check: 2160 Weight: 1.00 Name: CaM2 Len: 148 Check: 1261 Weight: 1.00 Name: CaM3 Len: 148 Check: 6090 Weight: 1.00 // 1 50 CaM1 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD CaM2 ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQD CaM3 ADQLTEEQIAEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVD 51 100 CaM1 MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI CaM2 MINEVDADGNGTIDFPEFLTMMEAFRVFDKDGNGYISAAELRHVMTNLGE CaM3 EMIREADIDGDGQVNYEEFVQMMTAK~~~~~~~~~~~~~~~~~~~~~~~~ 101 148 CaM1 SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK CaM2 KLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK~~~~~~~~~~~~~~ CaM3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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