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BioExtract Server Workflow Tutorial

Created: 2009-08-07 16:20:06 | Last updated: 2009-08-07 16:25:46

Credits: Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word 2007 document

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BioExtract Server Workflow Tutorial

Created: 2009-08-07 16:04:23 | Last updated: 2009-08-07 16:23:53

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Liliopsida Protein Alignment (6)

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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.

Created: 2010-01-13 | Last updated: 2010-11-17

Credits: Carol Lushbough

Phylogeny Bootstrapped Algorithm (2)

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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

Created: 2010-01-13 | Last updated: 2010-11-17

Credits: Carol Lushbough

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: Kendra Giesey Yosr Bouhlal BioExtract Server for Genomics

NCBI Protein Clustal Omega Alignment (1)

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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...

Created: 2012-08-31

Credits: Carol Lushbough

Non-redundant protein alignments (1)

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Execute BLASTP program to search protein databases using a protein query: Input file from iPlant Discovery Environment Save the data extract of similar sequences created by BLASTP Execute XMKNR to a compute a non-redundant set from a large collection of protein sequences. Input from the data extract created by BLASTP. Perform multiple sequence alignments using Clustal Omega and TCoffee Input from data extract created by XMKNR To execute this workflow, you need to be logged into the Bio...

Created: 2012-12-19 | Last updated: 2012-12-19

Credits: Carol Lushbough

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

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

Credits: zohim Carol Lushbough Bioextract BioExtract Server for Genomics