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Items tagged with "bioextract" (6)

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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 (4)

Workflow Liliopsida Protein Alignment (6)

Created: 13/01/10 @ 18:42:35 | Last updated: 17/11/10 @ 13:46:04

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 571 times | Downloaded: 109 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 Protein Mutation Analysis Using the BioExt... (1)

Created: 22/07/10 @ 20:20:07 | Last updated: 22/07/10 @ 20:29:56

Credits: User Kendra Giesey User Yosr Bouhlal Network-member BioExtract Server for Genomics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow, created using the BioExtract Server, contains a protein query (using the NCBI Protein Database), Blastp, ClustalW, Transeq, Garnier, PepWindowWall, PepInfo, and Octanol. For this workflow, a mutated protein sequence needs to be selected. Once the corresponding non-mutated sequence has been queried, the Blastp tool can be used to find sequences similar to the one queried, and the ClustalW tool can be used to analyze whether the mutation is conserved within species.  The Tra...

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

Viewed: 51 times | Downloaded: 23 times

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Workflow NCBI Protein Clustal Omega Alignment (1)

Created: 31/08/12 @ 19:18:55

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Searches NCBI Proteins for a given organism and protein. User VMatch (xmknr) Vmatch, a versatile software tool for efficiently solving large scale sequence matching tasks to remove possible dubplcate and clustal omega to generate a multiple sequence alignment. Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make u...

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

Viewed: 7 times | Downloaded: 0 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.

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

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