Workflow Entry: Nucleotide InterProScan for the BioExtract Server

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 Gene Ontology terms. Because InterProScan is a protein search tool,  the protein translation of a nucleotide sequence must be used.

Implementation:

1. Query NCBI Nucleotide Core for a specific sequence (e.g. Accession = ab070068)

2.  Execute EMBOSS getorf tool (emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html) to find the ORF protein translations.

3. Execute NCBI BlastP to perform a search using the ORF protein translations to identify sequences which have some relationship with known protein space.

4. Save the set of records identified by the blastp search.

5. Execute EBI's InterProScan tool ((http://www.ebi.ac.uk/Tools/webservices/services/interproscan) to access InterProScan.

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