Protein_alignment_transmembrane

Created: 2008-06-01 12:20:29

Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges:

  1. Sequence similarity search (SSS) to find homologues
  2. Fetch sequences of hits
  3. Multiple sequence alignment (MSA) of hit sequences
  4. EMBOSS tmap with alignment from 3.

Uses the EBI web services:

  1. WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta)
  2. WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch)
  3. WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2)
  4. Soaplab EMBOSS tmap

Note: currently this workflow does not attempt to add the query sequence into the set of sequences passed to the multiple alignment. Thus it is most suitable for searches using entires which are persent in the searched database (i.e. will be included via the self hit).

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An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers...

Created: 2009-04-07

Credits: User Hamish McWilliam

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This workflow performs "parallel" generic protein sequence analysis. In order to do that a list of known protein identifiers chosen by the biologist enters into the software to perform different multiple sequence alignments and finally phylogenetic analysis.

Created: 2010-06-29 | Last updated: 2010-08-31

Credits: User Achille Zappa

Attributions: Workflow EBI_ClustalW_alignment_tree