Protein_search_fetch_align_tree

Created: 2009-04-07 20:13:19

An implmentation of the classical sequence analysis workflow:

  1. Find homologues (sequence similarity search)
  2. Fetch homologues
  3. Align homologues (multiple sequence alignment)
  4. Produce phylogenetic tree

In this implementation the EBI webservices are used:

  1. WU-BLAST (WSWUBlast) blastp vs. UniProtKB
  2. dbfetch (WSDbfetch)
  3. ClustalW (WSClustalW2)
  4. 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 of existing database entries.

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Workflow Protein_alignment_transmembrane (1)

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Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: Sequence similarity search (SSS) to find homologues Fetch sequences of hits Multiple sequence alignment (MSA) of hit sequences EMBOSS tmap with alignment from 3. Uses the EBI web services: WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/servic...

Created: 2008-06-01

Credits: User Hamish McWilliam

Attributions: Workflow EBI_FASTA Workflow EBI_ClustalW2 Workflow EBI_dbfetch_fetchBatch

Workflow Workflow for Automated Comparative Protein... (2)

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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