Group: Baywatch Solutions

Overview

MyExperiment Group for the Team Baywatch (Solutions).

Newcastle University, 2010 MSc Bioinformatics e-Science Group B.

2010 Prize Winners!!!

 

Created at: Wednesday 10 March 2010 18:39:50 (UTC)

Unique name: teambncl

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  1. Avatar
    Andrew David King shared Fetch EMBL File
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    Fetches an EMBL file using the EMBL id. Creates file to a specified location.
    Wednesday 08 May 2013 14:52:01 (UTC)
  2. Avatar
    Andrew David King shared Fetch Fasta and Genbank files
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    Fetches fasta and genbank files for a given identifier., e.g., CP000256
    Wednesday 08 May 2013 14:52:01 (UTC)
  3. Avatar
    Andrew David King shared KEGG Pathway Analysis
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    The KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt unip …
    Wednesday 08 May 2013 14:52:01 (UTC)
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    Andrew David King shared Test for Orthologues
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    Warning: The files are hardcoded in to the beanshell of this workflow. Given an orthlog file for an organism from http://www.ebi.ac.uk/integr8/FtpSearch.do ? orgProteomeId=22602, find proteins that are orthologous to proteins in another oragnsims, e.g., B.subtils. Outputs percent.
    Wednesday 08 May 2013 14:52:01 (UTC)
  5. Avatar
    Fergus shared KEGG pathway analysis
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    The KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt unip …
    Wednesday 08 May 2013 14:52:01 (UTC)
  6. Avatar
    Andrew David King shared BlastandParse1
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    This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on th …
    Wednesday 08 May 2013 14:52:00 (UTC)
  7. Avatar
    Andrew David King shared BlastandParse2
    Thumb
    This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on th …
    Wednesday 08 May 2013 14:52:00 (UTC)
  8. Avatar
    Andrew David King created the Baywatch Solutions group
    Wednesday 10 March 2010 18:39:50 (UTC)

6 members

10 shared items

This group has been credited 9 times

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Workflow

Workflow Fetch EMBL File (1)

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Fetches an EMBL file using the EMBL id. Creates file to a specified location.

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Workflow

Workflow Fetch Fasta and Genbank files (1)

Thumb
Fetches fasta and genbank files for a given identifier., e.g., CP000256

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Workflow

Workflow BlastandParse1 (1)

Thumb
This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Attributions: Workflow fetchEnsemblSeqsAndBlast

Workflow

Workflow BlastandParse2 (1)

Thumb
This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Attributions: Workflow fetchEnsemblSeqsAndBlast

Workflow

Workflow Run MGCAT for Global Sequence Comparison (1)

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Runs the M-GCAT tool for Global Sequence Comparison. M-GCAT: http://alggen.lsi.upc.es/recerca/align/mgcat/ intro-mgcat.html

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Workflow

Workflow KEGG Pathway Analysis (1)

Thumb
The KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt uniprot: It performs this using the web service bconv, provided by the KEGG database (Kanehisa et a...

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Workflow

Workflow Test for Orthologues (1)

Thumb
Warning: The files are hardcoded in to the beanshell of this workflow. Given an orthlog file for an organism from http://www.ebi.ac.uk/integr8/FtpSearch.do? orgProteomeId=22602, find proteins that are orthologous to proteins in another oragnsims, e.g., B.subtils. Outputs percent.

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Workflow

Uploader

Workflow KEGG pathway analysis (1)

Thumb
The KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt uniprot: It performs this using the web service bconv, provided by the KEGG database (Kanehisa et al., 2010), described in the KEGG API available at: http://www.genome.jp/kegg/docs/keggapi...

Created: 2010-03-19

Credits: Network-member Baywatch Solutions


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