Workflow Entry: Nucleotide_InterProScan

Run InterProScan using a nucleotide sequence as input.

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. Since InterProScan is a protein search tool to use it with a nucleotide sequence, the sequence must be translated into a protein sequence. There are a number of ways of doing this, depending on the properties of the nucleotide sequence, in this case a simple open reading frame (ORF) model is used to obtain the candidate translations. These translations are filtered for length (>80aa) and a search against UniProtKB (http://www.uniprot.org/) is performed to ensure that only sequences which have some relationship with known protein space, on which the signatures used are based, are passed to InterProScan. Once the set of translations has been filtered the remaining sequences as passed on to InterProScan for analysis.

Note: the coordinates in the InterProScan output are in protein coordinates relative to the input translated sequence, to map these on to the input nucleotide sequence see the fasta header of the corresponding translated ORF where the nucleotide coordinates are shown.

This implementation uses:

1. EBI’s WSDbfetch web service (http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) to retreive enties specified by database identifer.

2. EMBOSS seqret tool (http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html) via Soaplab (http://www.ebi.ac.uk/Tools/webservices/soaplab/overview) to ensure input sequences are in an appropriate format (i.e. fasta format).

3. EMBOSS getorf tool (http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html) via Soaplab (http://www.ebi.ac.uk/Tools/webservices/soaplab/overview) to find the ORFs, perform the translation and filter the translations for length.

4. EBI’s WSNCBIBlast web service (http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast) to perform the filtering BLAST search against UniProtKB.

5. EBI’s WSInterProScan web service (http://www.ebi.ac.uk/Tools/webservices/services/interproscan) to access InterProScan for the final search.

and is based on the proceedure described for nucleotide InterProScan searches described on the WSInterProScan web pages (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan).