BioBind - GCG to EMBOSS Conversion

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GCG to EMBOSS Conversion

In 1985 the Genetics Computing Group in Wisconsin, USA, developed some bioinformatics tools and created the GCG software package. This suite was further enhanced a decade later as European developers started contributing sequence analysis tools as parted of the Extended GCG (EGCG) package.

EMBOSS was designed in 1999 by some of the EGCG developers with many of the same principles that can be found in the GCG package. The EMBOSS suite is designed as a collection of programs that can be used together to create a flexible analysis pipeline. There are no arbitrary size limits on sequence length and as EMBOSS reads and writes 42 different formats, it is easy to input and output files created from or for other software packages.

For those GCG users who have started using the BioBind product, this conversion chart should help you make the switch as easily and efficiently as possible. You will find many equivalences between the two software packages, although you currently will also find areas where there is no GCG equivalent for an EMBOSS program and vice versa. Each EMBOSS program contains a one line description to identify it. This description appears at the start of each application.

EMBOSS applications will prompt for all information required for it to execute. Additional prompts may be accessible using the -opt flag after the program name on the command line. The default option is displayed in square brackets ([ ]). To accept it, hit <return> otherwise type in whatever you like. Output file names often have as their suffix the name of the relevant application. To halt a program in EMBOSS hit ctrl C.

assemble	merger Merges two overlapping sequences into one. Produces a merged file and an alignment file. Matrix options accessible using the -opt flag.	$ merger Merge two overlapping nucleic acid sequences Input sequence: cam1.fasta Second sequence: cam2.fasta Output sequence [cam1.fasta]: cam_both.fasta Output alignment [cam1.out2]: cam_both.aln
backtranslate	backtranseq Translates protein back into a nucleotide sequence. Default codon usage table is the standard human one. To alter this use the -opt flag.	$ backtranseq Back translate a protein sequence Input sequence: calm_human Output sequence [calm_human.fasta]:
bestfit	water/matcher Finds the best local alignment(s) between two sequences. matcher (Huang & Miller algorithm) provides a faster match and should be used for longer sequences. water (Smith-Waterman algorithm) is more accurate and should be used for shorter sequences. Matrix options for matcher are available using the -opt flag	$ matcher Finds the best local alignments between two sequences Input sequence: cam1_long.fasta Second sequence: cam2_long.fasta Output alignment [cam1_1-429.matcher]: $ water Smith-Waterman local alignment. Input sequence: cam1.fasta Second sequence(s): cam2.fasta Gap opening penalty [10.0]: Gap extension penalty [0.5]: Output alignment [cam1.water]:
breakup	splitter Takes a sequence and splits it into smaller overlapping sequences. Use the -opt flag to select the size of each fragment.	$ splitter Split a sequence into (overlapping) smaller sequences Input sequence(s): cam1.fasta Output sequence [cam1.fasta]:
chopup	It is not necessary to have a separate program in EMBOSS for this, as all programs read and write a number of different file formats.
codonfrequency	chips/cusp/compseq chips calculates the effection number of codons used (Wright Nc statistic). cusp creates a codon usage table from coding sequence (CDS). compseq counts the composition of user-specifed words within the sequence. Use the -opt flag for further word specification.	$ chips Codon usage statistics Input sequence(s): cam1.fasta Output file [cam1_1-429.chips]: $ cusp Create a codon usage table Input sequence(s): cam1.fasta Output file [cam1_1-429.cusp]: $ compseq Counts the composition of dimer/trimer/etc words in a sequence Input sequence(s): cam1.fasta Word size to consider (e.g. 2=dimer) [2]: Output file [cam1_1-429.composition]:
codonpreference	syco/wobble syco identifies coding sequence from codon frequency bias information (Gribskov statistic). Further options for plot specification can be retrieved using the -opt flag. wobble plots a graph of the third "wobble" codon in a sequence. Use the -opt flag to alter the window size.	$ syco Synonymous codon usage Gribskov statistic plot Input sequence: cam1.fasta Graph type [x11]: ps Created syco.ps $ wobble Wobble base plot Input sequence: cam1.fasta Graph type [x11]: ps Output file [cam1_1-429.wobble]: Created wobble.ps
coilscan	pepcoil Identifies coiled coil regions in a protein sequence (Lupas, van Dyke & Stock algorithm).	$ pepcoil Predicts coiled coil regions Input sequence(s): calm_human Window size [28]: Output file [calm_human.pepcoil]:
compare	dottup/dotmatcher Comparison of similar regions across two sequences displayed in graphcal format. dottup is designed for identical matches, and dotmatcher for regions of similarity. Use the -opt flag to select matrix options.	$ dottup Displays a wordmatch dotplot of two sequences Input sequence: cam1.fasta Second sequence: cam2.fasta Word size [10]: Graph type [x11]: ps Created dottup.ps $ dotmatcher Displays a thresholded dotplot of two sequences Input sequence: cam1.fasta Second sequence: cam2.fasta Graph type [x11]: ps Created dotmatcher.ps
composition	compseq/pepstats compseq counts the composition of user-specifed words within the sequence. Use the -opt flag for further word specification. pepstats calculates peptide sequence composition.	$ compseq Counts the composition of dimer/trimer/etc words in a sequence Input sequence(s): cam1.fasta Word size to consider (e.g. 2=dimer) [2]: Output file [cam1_1-429.composition]: $ pepstats Protein statistics Input sequence(s): calm_human Output file [calm_human.pepstats]:
consensus	prophecy Creates a matrix or profile from a multiple alignment.	$ prophecy Creates matrices/profiles from multiple alignments Input sequence set: prot2.fasta Profile type F : Frequency G : Gribskov H : Henikoff Select type [F]: Enter a name for the profile [mymatrix]: Enter threshold reporting percentage [75]: Output file [prot2.prophecy]:
correspond	codecmp Compares codon frequency matrices.	$ codcmp Codon usage table comparison Codon usage file [Ehum.cut]: Second Codon usage file [Ehum.cut]: Eacc.cut Output file [outfile.codcmp]:
corrupt	msbar Randomly mutates a sequence. Use the -opt flag to mutate in frame.	$ msbar Mutate sequence beyond all recognition Input sequence(s): cam1.fasta Number of times to perform the mutation operations [1]: Point mutation operations 0 : None 1 : Any of the following 2 : Insertions 3 : Deletions 4 : Changes 5 : Duplications 6 : Moves Types of point mutations to perform [0]: Block mutation operations 0 : None 1 : Any of the following 2 : Insertions 3 : Deletions 4 : Changes 5 : Duplications 6 : Moves Types of block mutations to perform [0]: Codon mutation operations 0 : None 1 : Any of the following 2 : Insertions 3 : Deletions 4 : Changes 5 : Duplications 6 : Moves Types of codon mutations to perform [0]: Output sequence [cam1_1-429.fasta]:
dataset	dbiblast/dbigcg/dbifasta/dbiflat Indexes the relevant database for use with EMBOSS.
distances	no direct equivalent See the PHYLIP package offered as part of your BioBind software options.
diverge	no direct equivalent See the PHYLIP package offered as part of your BioBind software options.
dotplot	dottup/dotmatcher See comparison
extractpeptide	transeq Translates a nucleotide sequence into protein. Use the -opt flag to specify information on the region, frame and genetic code.	$ transeq Translate nucleic acid sequences Input sequence(s): cam1.fasta Output sequence [cam1_1-429.pep]:
fetch	seqret/seqretsplit seqret retrieves sequences from a database using the EMBOSS uniform sequence address. It can also by used with an input file to alter its format. seqretsplit splits a multi-sequence files into individual files containing a single sequence.Use the -opt flag to retrieve only the first sequence in a file.	$ seqretsplit Reads and writes (returns) sequences in individual files Input sequence(s): prot2.fasta Output sequence [calm_human.fasta]:
findpatterns	fuzznuc/fuzzpro Fuzzy search of a pattern against a sequence on selection of sequences. Search allows mismatches. fuzznuc searches nucleotide and fuzzpro protein sequences.	$ fuzznuc Nucleic acid pattern search Input sequence(s): cam1.fasta Search pattern: AGGT Number of mismatches [0]: 1 Output report [cam1_1-429.fuzznuc]: $ fuzzpro Protein pattern search Input sequence(s): prot2.fasta Search pattern: PATTERN Number of mismatches [0]: 3 Output report [calm_human.fuzzpro]:
frames	plotorf/showorf Plots or displays open reading frames. plotorf uses ATG as a start and TAA, TAG, TGA as stop codons and displays the results as a graphic. showorf writes out the results of a frame translation as text. Use the -opt flag for more options.	$ plotorf Plot potential open reading frames Input sequence: cam1.fasta Graph type [x11]: ps Created plotorf.ps $ showorf Pretty output of DNA translations Input sequence: cam1.fasta Select Frames To Translate 0 : None 1 : F1 2 : F2 3 : F3 4 : R1 5 : R2 6 : R3 Select one or more values [1,2,3,4,5,6]: Output file [cam1_1-429.showorf]:
from EMBL fromFasta fromGenbank fromIG fromStaden fromtrace	all All EMBOSS applications read and write a variety of file formats, so an individual conversion program is not necessary.
gap	stretcher/needle Finds the best global alignment between two sequences. stretcher (Myers & Miller algorithm) provides a faster match and should be used for longer sequences. needle (Needleman-Wunsch algorithm) is more accurate and should be used for shorter sequences. Matrix options for stretcher are available using the -opt flag	$ stretcher Finds the best global alignment between two sequences Input sequence: cam1_long.fasta Second sequence: cam2_long.fasta Output alignment [cam1_1-429.stretcher]: $ needle Needleman-Wunsch global alignment. Input sequence: cam1.fasta Second sequence(s): cam2.fasta Gap opening penalty [10.0]: Gap extension penalty [0.5]: Output alignment [cam1_1-429.needle]:
gapshow	plotcon Plots the quality of alignment conservation across a sliding window. Use the -opt flag to alter the comparison matrix.	$ plotcon Plots the quality of conservation of a sequence alignment Input sequence set: emma.aln Window size [4]: Graph type [x11]: ps Created plotcon.ps
getseq	newseq Enter a short sequence into the program for use as an input file in other applications.	$ newseq Type in a short new sequence. Name of the sequence: Test Description of the sequence: Test Protein Sequence Type of sequence N : Nucleic P : Protein Type of sequence [N]: P Output sequence [outfile.fasta]: Test.fasta Enter the sequence: wearethediddymenthediddymenthediddymen
growtree	no direct equivalent Use emma as the interface to ClustalW or the PHYILP option on your BioBind software.
helicalwheel	pepwheel Plots a protein sequence as a helix.Use the -opt flag to specify the output display.	$ pepwheel Shows protein sequences as helices Input sequence: calm_human Graph type [x11]: ps Created pepwheel.ps
hmmerAlign hmmerBuild hmmerCalibrate hmmerFetch hmmerIndex hmmerPfam hmmerSearch	no direct equivalent The HMMER programs are available as an option with your BioBind software.
hthscan	helixturnhelix Searches for 22 residue helix turn helix motifs in a protein sequence (Dodd & Egan).Use the -opt flag to search using their 20 residue region and further specify calculation parameters.	$ helixturnhelix Report nucleic acid binding motifs Input sequence(s): calm_human Output report [calm_human.hth]:
isoelectric	iep Calculates the isoelectric point of a protein.	$ iep calm_human Calculates the isoelectric point of a protein Output file [calm_human.iep]:
lookup	whichdb Does not offer all the parameters that lookup does, but will find identifers or acccession numbers in a database, and optionally retrieve the sequence.	$ whichdb Search all databases for an entry ID or Accession number: p62158 Output file [outfile.whichdb]: Output file [cam1_1-429.restover]:
map / mapplot / mapsort	restrict/remap/restover Calculates restriction maps based on the entries in the REBASE restriction enzyme database. Displays peptide translation of open reading frame. remap is the most felxible of these applications. Use the -opt flag to force specific cutters.	$ restrict cam1.fasta Finds restriction enzyme cleavage sites Minimum recognition site length [4]: Comma separated enzyme list [all]: Output report [cam1_1-429.restrict]: $ remap Display a sequence with restriction cut sites, translation etc.. Input sequence(s): cam1.fasta Comma separated enzyme list [all]: Minimum recognition site length [4]: Output file [cam1_1-429.remap]: $ restover Finds restriction enzymes that produce a specific overhang Input sequence(s): cam1.fasta Overlap sequence: overhang.fasta Output file [cam1_1-429.restover]:
melttemp	dan Calculates the melting temperature of a DNA or RNA sequence (Breslauer and Baldino statistics). Use the -opt flag to further specify calculations.	$ dan Calculates DNA RNA/DNA melting temperature Input sequence(s): cam1.fasta Enter window size [20]: Enter Shift Increment [1]: Enter DNA concentration (nM) [50.]: Enter salt concentration (mM) [50.]: Output report [cam1_1-429.dan]:
MEME	no direct equivalent See the MEME application included as an option in your BioBind software.
moment	hmoment Calculates the hydrophobic moment of protein. Use the -opt flag to specify the angle of rotation.	$ hmoment Hydrophobic moment calculation Input sequence(s): calm_human Output file [calm_human.hmoment]:
motifs	patmatmotifs/pscan patmatmotifs searches the PROSITE database for patterns. Use the -opt flag to specify patterns. pscan searches the PRINTS database for fingerprint motifs.	$ patmatmotifs Search a PROSITE motif database with a protein sequence Input sequence: calm_human Output report [calm_human.patmatmotifs]: $ pscan Scans proteins using PRINTS Input sequence(s): calm_human Minimum number of elements per fingerprint [2]: Maximum number of elements per fingerprint [20]: Output file [calm_human.pscan]:
names	infoseq Describes sequence attributes such as name, length, GC content.	$ infoseq Displays some simple information about sequences Input sequence(s): calm_human # USA Name Accession Type Length Description fasta::calm_human:CALM_HUMAN CALM_HUMAN P62158 P 148 Calmodulin (CaM).
nooverlap	diffseq Finds differences between two sequences. Use the -opt flag to output the information in columns.	$ diffseq Find differences between nearly identical sequences Input sequence: cam1.fasta Second sequence: cam2.fasta Word size [10]: Output report [cam1_1-429.diffseq]: Output features [CaM1_1-429.diffgff]: Second output features [CaM2.diffgff]:
pepdata	getorf/sixpack Translates all six open reading frames. getorf displays selected translations. sixpack displays DNA sequence and peptide translation. Use the -opt flag for either program to specify the codon usage information.	$ getorf Finds and extracts open reading frames (ORFs) Input sequence(s): cam1.fasta Output sequence [cam1_1-429.orf]: $ sixpack Display a DNA sequence with frame translation and ORFs Input sequence: cam1.fasta Output file [cam1_1-429.sixpack]: Output sequence [cam1_1-429.fasta]:
pepplot	pepinfo + garnier pepinfo displays biophysical properties of the protein sequence and plots hydrophobicity (Kyte & Doolittle, Sweet & Eisenberg, Eisernberg). Use the -opt flag to select parameters for the hydrophobicity plots. garnier displays a secondary structure plot (Garnier, Ogusthorpe & Robson)	$ pepinfo Plots simple amino acid properties in parallel Input sequence: calm_human Graph type [x11]: ps Output file [calm_human.pepinfo]: Created pepinfo.ps $ garnier Predicts protein secondary structure Input sequence(s): calm_human Output report [calm_human.garnier]:
peptidemap	digest Peptide full or partial digest of a protein sequence.	$ digest Protein proteolytic enzyme or reagent cleavage digest Input sequence: calm_human Enzymes and Reagents 1 : Trypsin 2 : Lys-C 3 : Arg-C 4 : Asp-N 5 : V8-bicarb 6 : V8-phosph 7 : Chymotrypsin 8 : CNBr Select number [1]: Output report [calm_human.digest]:
peptidestructure / plotstructure	garnier Displays secondary structure plot (Garnier, Ogusthorpe & Robson)	$ garnier Predicts protein secondary structure Input sequence(s): calm_human Output report [calm_human.garnier]:
pileup	emma Wrapper to the ClustalW multiple sequence alignment program. Accepts all EMBOSS input formats.	$ emma Multiple alignment program - interface to ClustalW program Input sequence(s): prot_all.fasta Output sequence [cam2.aln]: Dendogram output filename [cam2.dnd]: CLUSTAL W (1.83) Multiple Sequence Alignments Sequence type explicitly set to Protein Sequence format is Pearson Sequence 1: CaM2 148 aa Sequence 2: CaM3 148 aa Sequence 3: CaM1 148 aa Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 93 Sequences (1:3) Aligned. Score: 100 Sequences (2:3) Aligned. Score: 97 Guide tree file created: [00002524C] Start of Multiple Alignment There are 2 groups Aligning... Group 1: Sequences: 2 Score:2070 Group 2: Sequences: 3 Score:1098 Alignment Score 1439 GCG-Alignment file created [00002524B]
plasmidmap	lindna/cirdna Display of linear and circular DNA. Also, the Jemboss DNA Editor is a graphical interface to display and edit linear and circular.
plotsimilarity	plotcon See gapshow
pretty / prettybox	cons/prettyplot/showalign cons calculates a consensus from a multiple alignment using specified parameters. prettyplot displays an alignment with specified colours and boxed in display. showalign displays the alignment in editable text format. Use the -opt flag for all three programs to set values. These programs are all incorporated in the Jemboss Alignment Editor together with additional capabilities.
prime	eprimer3 Included in your BioBind software. Allows selection of a variety of different primers under several conditions. Use the -opt flag to alter parameters.	$ eprimer3 Picks PCR primers and hybridization oligos Input sequence(s): cam3.fasta Output file [cam3.eprimer3]:
profilegap / profilemake	prophet/prophecy prophecy creates matrices or profiles from multiple alignments. prophet reads in these files to create gapped alignment of proteins.	$ prophecy Creates matrices/profiles from multiple alignments Input sequence set: emma.aln Profile type F : Frequency G : Gribskov H : Henikoff Select type [F]: Enter a name for the profile [mymatrix]: Enter threshold reporting percentage [75]: Output file [emma.prophecy]: $ prophet Gapped alignment for profiles Input sequence(s): calm_human Profile or matrix file: emma.prophecy Gap opening coefficient [1.0]: Gap extension coefficient [1.0]: Output file [calm_human.prophet]:
profilescan	patmatdb Uses a motif to search a protein sequence.	$ patmatdb Search a protein sequence with a motif Input sequence(s): emma.aln Protein motif to search for: HATS Output report [cam2.patmatdb]:
profilesearch	profit Scans a sequence or database with a matrix or profile. Uses the matrix file created by prophecy.	$ profit Scan a sequence or database with a matrix or profile Profile or matrix file: emma.prophecy Input sequence(s): calm_human Output file [emma.profit]:
reformat	seqret Reformatting files is redundant in EMBOSS as each application reads and write a variety of different formats. However, if anything needs converting, seqret will do it.	$ seqret Reads and writes (returns) sequences Input sequence(s): calm.gcg Output sequence [calm_human.fasta]:
repeat	equicktandem/etandem/einverted/palindrome Searches for tandem repeats, inverted or palindromic sequences in a nucleotide input file.	$ equicktandem Finds tandem repeats Input sequence: cam1.fasta Maximum repeat size [600]: Threshold score [20]: Output report [cam1_1-429.qtan]: $ etandem Looks for tandem repeats in a nucleotide sequence Input sequence: cam1.fasta Minimum repeat size [10]: Maximum repeat size [10]: Output report [cam1_1-429.tan]: $ einverted Finds DNA inverted repeats Input sequence: cam1.fasta Gap penalty [12]: Minimum score threshold [50]: Match score [3]: Mismatch score [-4]: Output file [cam1_1-429.inv]: $ palindrome Looks for inverted repeats in a nucleotide sequence Input sequence(s): cam1.fasta Enter minimum length of palindrome [10]: Enter maximum length of palindrome [100]: Enter maximum gap between repeated regions [100]: Number of mismatches allowed [0]: Output file [cam1_1-429.pal]: Report overlapping matches [Y]:
replace	biosed/degapseq biosed replaces specified characters in a text file. degapseq is specific for removing gaps.	$ biosed Replace or delete sequence sections Input sequence(s): cam1.fasta Sequence section to match [N]: Replacement sequence section [A]: Output sequence [cam1_1-429.fasta]: $ degapseq Removes gap characters from sequences Input sequence(s): cam1.fasta Output sequence [cam1_1-429.fasta]:
reverse	revseq Reverses and complements a sequence. Almost any program in the suite can reverse and complement a sequence using the -reverse option. Alternatively the [start:end:reverse] syntax will accomplish the same task.	$ revseq Reverse and complement a sequence Input sequence(s): cam1.fasta Output sequence [cam1_1-429.rev]:
sample	extractseq Extracts specific regions from a sequence. Use the -opt flag to save them to a separate file.	$ extractseq Extract regions from a sequence Input sequence: cam1.fasta Regions to extract (eg: 4-57,78-94) [1-429]: 1-25 Output sequence [cam1_1-429.fasta]:
seg	maskseq Masks low complexity regions within a sequences. Use the -opt flag to select a region to mask.	$ maskfeat Mask off features of a sequence. Input sequence(s): cam1.fasta Output sequence [cam1_1-429.fasta]:
shuffle	shuffleseq Shuffles one or a set of sequences.	$ shuffleseq Shuffles a set of sequences maintaining composition Input sequence(s): calm_human Output sequence [calm_human.fasta]:
spscan	sigcleave Searches for signal sequences in proteins. Use the -opt flag to specify a prokaryotic sequence.	$ sigcleave Reports protein signal cleavage sites Input sequence(s): calm_human Minimum weight [3.5]: Output report [calm_human.sig]:
stemloop	etandem/palindrome See repeat
testcode	wobble See codonpreference
toFASTA toPIR toIG toSTADEN	seqret See fromEMBL
translate	transeq See extractpeptide.
window + statplot	freak Calculates the base or residue frequency of a sequence. Use the -opt flag to select the window type for calculation of the plot.	$ freak Residue/base frequency table or plot Input sequence(s): cam1.fasta Residue letters [gc]: Output file [cam1_1-429.freak]:
gcghelp	tfm Stands for "the fine manual" and contains the indivudal program documentation. Type *tfm* followed by the program name.	$ tfm stretcher Displays a program's help documentation manual