BioBind - EMBASSY

>Home

>EMBASSY

In order to enhance the functionality of the EMBOSS suite of applications, further programs have been added to your BioBind software. These come in the form of EMBASSY packages and databases. The majority of these are distributable without restriction. Others require a licence for commercial users and whilst BioBind has incorporated the functionality to allow download of all these products, those for whom a licence is necessary must be in possesion of one before attempting to use these additional features.

It should be noted that as this is third party software, copyright and responsibility for maintenance of each application is not an option for BioBind and whilst every effort is made to update these programs, some scenarios may be beyond our control.

EMBASSY

The EMBASSY software packages have been incorporated into the EMBOSS suite to share the same look and feel and these applications are accessed in exactly the same way as any others.

ClustalW

ClustalW is the program that provides the clustering algorithm behind the EMBOSS program emma. It carries out pairwise analysis of each combination of sequences in a multiple file input and aligns them according to the distance matrix it creates on the basis of these global pairwise alignments. There are no restrictions on the use of this software for analysis purposes.

PHYLIP

The PHYlogeny Interface Package is a series of software applications designed to create phylogenies from sequences displaying homology. Methods of applications within the package include maximum likelihood, distance matrices and parsimony. Currently your BioBind software suite incorporates PHYLIP Version 3.5. There are no restrictions on the use of this software for analysis purposes.

Single files can be entered in the majority of formats as the software will automatically convert this to the correct format for the PHYLIP programs. It is, however, advisable that multiple sequence alignment files are input into these programs in the PHYLIP format. This can be selected when using emma in the Output Sequence Options.

Some of the more complex phylogenetic calculations will take a substantial amount of time and may not be suitable to run if you wish to use your software for other analyses in a particular period.

ESIM4

In addition to the EST-Genomic alignment software already available as EST2Genome, a further application will run a similar anyalsis. SIM4 also aligns expressed DNA sequences or fragments with genomic sequence using homology searching and information on intron/exon boundaries. There are no restrictions on the use of this software for analysis purposes.

This utility may be slightly faster than EST2Genome although the method it uses may mean the final result is less accurate for some alignments. Sequences may be input in any file format.

Domainatrix

This is a suite of programs developed for protein structural analysis. It offers both analysis and graphical visualisation. Currently your BioBind software suite incorporates Domainatrix Version 1.0. There are no restrictions on the use of this software for analysis purposes.

The suite makes use of cleaned data from the 3D protein structure databases PDB, SCOP and CATH. The input format of this data is specified for each program and it is often a format obtainable only as the output of second application. In order to clean the PDB, SCOP and CATH data for input pdbparse, scopparse and cathparse must be used on the relevant dataset.

HMMER

Hidden Markov Models are becoming increasingly common in a variety of bioinformatics systems and lend accuracy and flexibility to a search. The HMMer package offers applications for creating your own hidden Markov models from seed alignments and using them to search the database for distant homologies. There are no restrictions on the use of this software for analysis purposes.

As HMMer is a suite of interlinking modules, the input for some applications is the output of others. Sequence data may be input into ehmmbuild in any format. This creates an HMM file which can then be used as input for the other programs requiring it.

TOPO

This is a program for graphically displaying a transmembrane protein. It requires a sequence and specific information on the location of the transmembrane region before creating a coloured graphic. There are no restrictions on the use of this software for analysis purposes.

The program will read in any sequence format and accept transmembrane regions and signature sequences. The transmembrane regions must be entered as pairs of typed numbers separated by spaces. For example 20 42 49 61 would mean two membrane spanning regions, one crossing the membrane between residues 20-42 and the other between residues 49-61. In the Jemboss interface, residues positions should be separated by commas, thus regions 20-42 and 49-61 would be entered as 20,42,49,61.

Signature sequences should be specified in the same way with the typed numbers of the start and end residues of the signature. After the range the symbol representing the colour and shape of the residue should be entered. Thus 45 63 SY would indicate that there is a signature sequence between residues 45-63 and it should be represented on the graphical output by a yellow square. Full details of the symbol abbreviations can be found in the relevant documentation.

MEME

Multiple Em for Motif Elicitation is a motif search and discovery tool. It takes a training set of input sequences and searches them for repeat patterns. Motifs are returned as the exact sequence, with annotated variations and as a matrix. There are no restrictions on the use of this software for academic analysis purposes. Commercial users must licence this software a part of its terms of distribution.

The preferred format for input is fasta fomat, but it will allow a large number of alternative sequence formats. Input may be a training set of either all DNA sequences or all protein sequences.

Databases

A minority of EMBOSS applications involve scanning databases and in order for them to function, the appropriate database is distributed as part of your BioBind software package. There are no restrictions on the data we have chosen to accompany specific applications.

PRINTS

The PRINTS database is a curated repository of motifs identified as a series of elements known as fingerprints which characterise a protein family. These have been create by iterative scanning of the SwissProt and TrEMBL protein databases. The pscan application searches this database with a single input sequence to determine whether it contains any identified motifs.

PROSITE

The PROSITE database contained within this software suite consists of a series of patterns to determine the signatures of protein families. These signatures have been elucidated by iterative searching of the protein databases using patterns taken from seed alignments. The patmatmotifs application allows this database to be queried by a single input sequence in order to ascertain whether any signatures are present and possibly assign a new protein sequence to an existing family.

TRANSFAC

The Transfac database is a collection of transcription factors and promotor sites and is used by the tfscan application to determine whether there are any regulatory regions in an input DNA sequence. The version that accompanies your BioBind software is Version 4.0.

Subsequent versions are no longer avaiable for incorporation, although they are still available through the Transfac website. A previous version is free for registered academics, although the current version must be purchased. Rates differ for academic and commercial use.

Should you have access to a current version of Transfac, you can use it as the seearch repository for the tfscan application. Download the new datafiles to the specified path and then run tfextract on them in order to index the files corectly for use with tfscan.