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Items tagged with "phylogenetic tree" (8)

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Files (1)
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Blob BioExtract Server Workflow Tutorial

Created: 07/08/09 @ 16:20:06 | Last updated: 07/08/09 @ 16:25:46

Credits: User Carol Lushbough

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: 37 times | Downloaded: 29 times

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Workflows (6)
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Workflow Workflow for Protein Sequence Analysis (1)

Created: 09/01/08 @ 12:03:03 | Last updated: 09/01/08 @ 12:31:27

Credits: User M.B.Monteiro

Attributions: Workflow BLAST using DDBJ service Workflow Simplify a BLAST text file Workflow conditional branch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 4.0 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1795 times | Downloaded: 467 times

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Original Uploader

Workflow EBI_ClustalW2_phylogentic_tree (2)

Created: 07/04/09 @ 20:09:32

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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).

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 1 | Comments: 1 | Citations: 0

Viewed: 311 times | Downloaded: 115 times

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Original Uploader

Workflow EBI_ClustalW_alignment_tree (2)

Created: 31/05/08 @ 13:53:04 | Last updated: 03/12/10 @ 13:34:43

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree

License: Creative Commons Attribution 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 194 times | Downloaded: 89 times

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Original Uploader

Workflow Protein_search_fetch_align_tree (2)

Created: 07/04/09 @ 20:13:19

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree Workflow EBI_dbfetch_fetchBatch Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 463 times | Downloaded: 154 times

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Workflow Phylogeny Bootstrapped Algorithm (2)

Created: 13/01/10 @ 18:47:06 | Last updated: 17/11/10 @ 13:57:19

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Bootstrapped sequences algorithm reads in a data set, and produces multiple data sets from it by bootstrap resampling. http://pro.genomics.purdue.edu/cgi-bin/emboss/help/fseqboot

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 215 times | Downloaded: 135 times

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Original Uploader

Workflow MY_Multi_Alignment_Phylo (1)

Created: 03/11/09 @ 14:46:38

Credits: User Achille Zappa

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow performs a 'multiple' multiple sequence alignment and phylogenetic analysis.

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

Viewed: 155 times | Downloaded: 44 times

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Packs (1)
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Pack BioExtract Server Workflow Tutorial


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.

0 items in this pack

Comments: 0 | Viewed: 61 times | Downloaded: 14 times

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