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Items tagged with "tree" (8)

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Workflows (8)
Original Uploader

Workflow SifterWorkflow_Prod_Neu (2)

Created: 23/11/07 @ 16:42:24 | Last updated: 29/04/08 @ 10:37:12

Credits: User Anika Joecker

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Phylogenomic workflow with SIFTER. The workflow first runs an iterative Blast search against the RefSeq database (Pruitt et al. 2007) (only fully sequenced organisms) and filters the results to get putative orthologous and in-paralogous proteins. These sequences are used to build a multiple alignment with MAFFT (Katoh et al. 2005). After filtering out alignment columns with more than 60% gaps, a phylogenetic tree is build. If there are less than 20 proteins in the alignment Phyml (Guindon an...

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

Viewed: 479 times | Downloaded: 151 times

Tags (6):

Original Uploader

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

Tags (10):

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

Tags (7):

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

Tags (10):

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

Tags (15):

Original Uploader

Workflow fetch_fasta (1)

Created: 20/03/09 @ 11:22:45 | Last updated: 20/03/09 @ 11:29:16

Credits: User Jumblejumble

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain. Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree. The output is prese...

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

Viewed: 173 times | Downloaded: 81 times

Tags (11):

Original Uploader

Workflow M_Fetch_e-T_phylo_boot - (BETA) (1)

Created: 10/03/10 @ 15:44:02 | Last updated: 10/03/10 @ 15:49:06

Credits: User Achille Zappa User Hamish McWilliam

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

Viewed: 47 times | Downloaded: 19 times

Tags (12):

Original Uploader

Workflow Simple protein distance phylogeny workflow (1)

Created: 22/09/11 @ 16:47:46 | Last updated: 22/09/11 @ 16:47:49

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Performs a multiple alignment and makes a phylogeny using a distance method on a set of protein sequences  

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

Viewed: 25 times | Downloaded: 17 times

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