Workflows

Protein_search_fetch_align_tree (2)

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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: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST

EBI_ClustalW2_phylogentic_tree (2)

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Create a Neighbor-joining phylogenetic tree, with Kimura distance corrections, from a sequence alignment using the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2).

Created: 2009-04-07

Credits: Hamish McWilliam

EBI_ClustalW_alignment_tree (2)

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Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks.

Created: 2008-05-31 | Last updated: 2010-12-03

Credits: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree

M_Fetch_e-T_phylo_boot - (BETA) (1)

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This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.

Created: 2010-03-10 | Last updated: 2010-03-10

Credits: Achille Zappa Hamish McWilliam