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InviteGroup: BioExtract Server for Genomics
The BioExtract Server (http://bioextract.org) is designed to contribute to meeting this need by allowing researchers via a Web browser to query multiple data sources, save query results as searchable data sets, execute local and Web-accessible analytic tools, and create computational workflows. The purpose of this group is to being the process of allowing researchers to share BioExtract Server workflows.
Created at: Thursday 30 October 2008 @ 16:39:23 (GMT)
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Created: 03/11/10 @ 17:23:21 | Last updated: 03/11/10 @ 17:23:22
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow was created to predict the effect of the mutation on the primary and the secondary structure of a mutated sacsin protein.
The genomic sequence bearing the mutation should be pasted on FASTA format as input for the Transeq tool. This sequence will be translated to protein and compared to the wild type protein, already extracted from NCBI database, through the Supermatcher tool. Variation(s) will be verified by multiple alignment using Blastp and ClustalW tools.
Prediction of th...
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Created: 20/06/11 @ 20:55:23 | Last updated: 05/07/11 @ 18:21:04
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 22/07/10 @ 20:20:07 | Last updated: 22/07/10 @ 20:29:56
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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Created: 17/06/10 @ 16:34:50 | Last updated: 19/07/10 @ 20:00:00
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow, created using the BioExtract Server, contains a nucleotide query (using the NCBI Core Nucleotide Database), Blastn (against the Homo sapiens genome), Blastn (against the Mus musculus genome), the Format Conversion tool, the Fetch Translator Tool, and ClustalW. This workflow was created following the analytical steps described in the journal article "Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced the...
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