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Items tagged with "clustalw" (5)

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Taverna 1

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Hamish McWilliam

EBI_ClustalW2 (v1)

Created: 31/05/08 @ 10:27:59 | Last updated: 02/06/08 @ 21:27:39

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Perform a ClustalW multiple sequence alignment using the EBI’s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

Original Uploader

Hamish McWilliam

EBI_ClustalW2_phylogentic_tree (v1)

Created: 31/05/08 @ 13:07:35

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 License

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).

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Taverna 1

Original Uploader

Hamish McWilliam

EBI_ClustalW_alignment_tree (v1)

Created: 31/05/08 @ 13:53:05 | Last updated: 31/05/08 @ 13:53:06

Credits: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree

License: Creative Commons Attribution 3.0 License

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.

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Taverna 1

Original Uploader

Hamish McWilliam

Protein_search_fetch_align_tree (v1)

Created: 31/05/08 @ 21:09:18

Credits: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST

License: Creative Commons Attribution 3.0 License

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 ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

Original Uploader

Hamish McWilliam

Protein_alignment_transmembrane (v1)

Created: 01/06/08 @ 12:20:30 | Last updated: 01/06/08 @ 12:20:31

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch

License: Creative Commons Attribution 3.0 License

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/webs...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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