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Items tagged with "bioextract" (8)

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Blob BioExtract Server Workflow Tutorial

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

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Pack BioExtract Server Workflow Tutorial


Created: 2009-08-07 16:04:23 | Last updated: 2009-08-07 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: 79 times | Downloaded: 23 times

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Workflows (6)

Workflow 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: User Carol Lushbough

Workflow 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: User Carol Lushbough

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 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: User Carol Lushbough

Workflow 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: User Carol Lushbough

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

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