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Items tagged with "multiple sequence alignment" (14)
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Created: 09/01/08 @ 12:03:03 | Last updated: 09/01/08 @ 12:31:27
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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.
Rating: 4.0 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 1615 times | Downloaded: 430 times Tags (10): |
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Created: 07/04/09 @ 20:06:03 | Last updated: 06/12/10 @ 11:00:19
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License: Creative Commons Attribution 3.0 Unported 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.
Note: the WSClustalW2 service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement ClustalW2 servi...
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 506 times | Downloaded: 240 times Tags (7): |
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Created: 31/05/08 @ 13:53:04 | Last updated: 03/12/10 @ 13:34:43
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License: Creative Commons Attribution 3.0 Unported 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.
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 176 times | Downloaded: 83 times Tags (10): |
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Created: 07/04/09 @ 20:13:19
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License: Creative Commons Attribution 3.0 Unported License
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...
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 419 times | Downloaded: 140 times Tags (15): |
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Created: 01/06/08 @ 12:20:29
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License: Creative Commons Attribution 3.0 Unported License
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...
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 190 times | Downloaded: 57 times Tags (16): |
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Created: 02/06/08 @ 21:28:56 | Last updated: 06/12/10 @ 11:39:52
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License: Creative Commons Attribution 3.0 Unported License
Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default.
Note: the WSKalign service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. Thi...
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 73 times | Downloaded: 45 times Tags (6): |
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Created: 03/06/08 @ 05:55:43 | Last updated: 06/12/10 @ 11:38:58
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License: Creative Commons Attribution 3.0 Unported License
Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool.
Note: the WSMafft service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MAFFT services (REST or SOAP) should be used instead.
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Created: 03/06/08 @ 06:16:22 | Last updated: 06/12/10 @ 11:04:03
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License: Creative Commons Attribution 3.0 Unported License
Perform a multiple sequence alignment using the MUSCLE tool (see http://www.drive5.com/muscle/). The EBI's WSMuscle web service (see http://www.ebi.ac.uk/Tools/webservices/services/muscle) is used.
Note: the WSMuscle service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MUSCLE services (REST or SOAP) should be used instead.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 109 times | Downloaded: 57 times Tags (6): |
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Created: 03/06/08 @ 06:31:37 | Last updated: 06/12/10 @ 11:02:53
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License: Creative Commons Attribution 3.0 Unported License
Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSTCoffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) is used.
Note: the WSTCoffee service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement T-COFFEE services (REST or SOAP) should be used instead.
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Created: 13/01/10 @ 18:42:35 | Last updated: 17/11/10 @ 13:46:04
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow retrieves Liliopsida chloroplast petb gene sequences from NCBI Nucleotide, removes duplicate sequences and saves the results at BioExtract Server. These results are then converted into GenBank format and fed into Fetch Translation, which removes the translation from the CDS coding region. Translations are then used to build a multiple alignment using ClustalW.
Rating: 4.0 / 5 (1 rating) | Versions: 6 | Reviews: 0 | Comments: 3 | Citations: 1 Viewed: 544 times | Downloaded: 106 times Tags (5): |
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Created: 06/12/10 @ 13:16:52
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License: Creative Commons Attribution 3.0 Unported License
Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).
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Created: 17/01/11 @ 16:48:40 | Last updated: 17/01/11 @ 16:48:37
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).
This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. Perform a ClustalW2 alignment using the EMBL-EBI’s C...
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Created: 07/08/09 @ 16:04:23 | Last updated: 07/08/09 @ 16:23:53
A tutorial to demonstrate how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.
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Created: 07/08/09 @ 16:20:06 | Last updated: 07/08/09 @ 16:25:46
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This tutorial demonstrates how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.
File type: Word 2007 document Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 29 times | Downloaded: 25 times Tags: |
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