Workflows

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Type: BioExtract Server

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 Nucleotide InterProScan for the BioExtract... (3)

Created: 16/04/09 @ 15:26:57 | Last updated: 01/07/09 @ 08:32:34

Credits: User Carol Lushbough User Hamish McWilliam

Attributions: Workflow Nucleotide_InterProScan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow can be downloaded and imported into the BioExtract Server at bioextract.org. This workflow is a BioExtract Server process similar to the Nucleotide InterProScan workflow designed and implement in Taverna by Hamish McWilliams. The InterProScan tool (http://www.ebi.ac.uk/Tools/InterProScan/) searches a protein sequence against a selection of protein domain, feature and family signature databases, and integrates the results giving potential assignments to InterPro entries and Gen...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 158 times | Downloaded: 91 times

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Workflow Multiple Protein Alignment Profiling(1) (4)

Created: 13/01/10 @ 18:52:45 | Last updated: 17/11/10 @ 14:13:20

Credits: User Carol Lushbough User Alan Williams

Attributions: Workflow A workflow version of the EMBOSS tutorial

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Designed from an example workflow at Traverna, this workflow retrieves a set of sequences from UniProt, then simultaneously scans for transmembrane regions and performs a multiple alignment using EMMA. The alignment is then plotted to a set of PNG images, followed by a profile analysis using prophecy and prophet tools.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 161 times | Downloaded: 61 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 SH2 domain screen in homo (1)

Created: 19/02/09 @ 16:34:22 | Last updated: 08/06/09 @ 10:30:49

Credits: User Youguruozhu

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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You can now Download this Workflow and import it into BioExtract Server at bioextract.org. This workflow retrieves a set of protein sequences containing SH2 domain in homo sapiens from NCBI GenBank Protein, then extracts the sequences of SH2 regions and performs a multiple alignment using EMMA and ClustalW. The alignment by EMMA is then plotted to PNG images, simultaneously creating a frequency matrix by prophecy. Finally scan a protein sequence queried with the frequency matrix using prophet.

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

Viewed: 159 times | Downloaded: 28 times

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Original Uploader

Workflow hbr (1)

Created: 29/06/09 @ 13:40:16

Credits: User Hbrphd

License: Creative Commons Attribution-Share Alike 3.0 Unported License

abcc1 CYP2D6 CYP2E1

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

Viewed: 15 times | Downloaded: 15 times

This Workflow has no tags!

Original Uploader

Workflow Blastn-ClustalW (1)

Created: 27/10/10 @ 15:23:00 | Last updated: 27/10/10 @ 15:23:01

Credits: User Kalpana

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow retrieves a sequence from NCBI Core Nucleotide, searches for similar sequences with Blastn, then feeds a set of Blastn results into the multiple alignment tool, ClustalW.

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

Viewed: 10 times | Downloaded: 11 times

This Workflow has no tags!

Original Uploader

Workflow Gene function prediction in Macaca Fasciculus (1)

Created: 27/03/11 @ 21:19:27 | Last updated: 27/03/11 @ 21:29:29

Credits: User Kalpana

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for ORF regions in a specific gene (TOM1L1 in Macaca fasciculus testis) to predict candidate protein coding regions. Results from blastp are used to find which frames are closest to existing proteins in other species. rpsblast is used to predict the domains and the protein families that these sequences may belong to. This is used to predict the function of the protein.

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

Viewed: 13 times | Downloaded: 5 times

This Workflow has no tags!

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 tblastx non-redundant alignment (1)

Created: 30/06/11 @ 15:26:13 | Last updated: 04/07/11 @ 16:51:41

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow carries out alignments using TCoffee and ClustalW2 for a set of non-redundant proteins where the starting point is a particular genomic coding sequence representing only one member of the gene family in a given species.   For the BioExtract Server implementation, the necessary steps for accomplishing this task involve: 1.   Selecting the NCBI tblastx tool and providing the accession number of the known nucleotide sequence record as input. 2.   The output from ...

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

Viewed: 25 times | Downloaded: 6 times

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