myExperiment - Groups

Taverna 2

Uploader

Andrew David King

Download

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: Baywatch Solutions

Attributions: fetchEnsemblSeqsAndBlast

Taverna 2

Uploader

Andrew David King

BlastandParse1 (1)

Download

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: Baywatch Solutions

Attributions: fetchEnsemblSeqsAndBlast

Taverna 2

Uploader

Fergus

KEGG pathway analysis (1)

Download

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: Baywatch Solutions

Taverna 2

Uploader

Andrew David King

KEGG Pathway Analysis (1)

Download

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: Baywatch Solutions

Taverna 2

Uploader

Andrew David King

Test for Orthologues (1)

Download

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.