Group: BioExtract Server for Genomics

Overview

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 (UTC)

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  1. 4438?size=48x48
    Dr Kaveh Ostad Ali Askari joined the BioExtract Server for Genomics group
    Sunday 05 February 2017 14:12:06 (UTC)
  2. 1835?size=48x48
    Yosr Bouhlal shared Biomart SNP
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    Monday 20 June 2011 20:55:26 (UTC)
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    Yosr Bouhlal shared Sacs Gene Muation Analysis
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    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 …
    Wednesday 03 November 2010 17:23:22 (UTC)
  4. 1835?size=48x48
    Yosr Bouhlal joined the BioExtract Server for Genomics group
    Monday 14 June 2010 18:03:04 (UTC)
  5. 484?size=48x48
    Carol Lushbough created the BioExtract Server for Genomics group
    Thursday 30 October 2008 16:39:23 (UTC)

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Workflow

Workflow RNA-Seq workflow with TopHat and Cufflinks... (1)

An example workflow demonstrating the RNA-seq analysis using Bioextract Server. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. (Ref: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html).

Created: 2013-11-09 | Last updated: 2014-04-10

Credits: User zohim User Carol Lushbough User Bioextract Network-member BioExtract Server for Genomics

Workflow

Workflow Protein Mutation Analysis Using the BioExt... (1)

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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...

Created: 2010-07-22 | Last updated: 2010-07-22

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

Workflow

Workflow Phylogenetic Study Using the Bio Extract S... (2)

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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...

Created: 2010-06-17 | Last updated: 2010-07-19

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


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