Current

News for 2009.

Due to changes in the available data access methods with the release of Ensembl 51 (18 November 2008), Ensembl Gene (ensemblgene) and Ensembl Transcript (ensembltranscript) in WSDbfetch SOAP and REST now only support returning the sequence data in fasta format.

Sample Java client now available for WSPhobius, a transmembrane domain and signal peptide prediction service.

C# sample clients now available for:

• WSMafft: multiple sequence alignment
• WSMPsrch: Smith-Waterman sequence similarity search
• WSMuscle: multiple sequence alignment
• WSPhobius: transmembrane domain and signal peptide prediction
• WSScanPS: Smith-Waterman sequence similarity search
• WSTCoffee: multiple sequence alignment

C# sample clients now available for:

• WSCensor: repetative sequence element identification and masking
• WSDaliLite: pairwise structure alignment
• WSKalign: multiple sequence alignment
• WSMaxSprout: protein backbone and side chain co-ordinates from a C(alpha) trace

Entries from InterPro Matches Complete (iprmc) and InterPro Matches Complete UniParc (iprmcuniparc) are now available via WSDbfetch.

These InterPro Matches databases contain pre-calculated InterProScan results for the protein sequences in the UniProtKB and UniParc at the time of the InterPro release.

The data is available from WSDbfetch in three formats:

1. iprmc: HTML entry as available in SRS@EBI.
2. iprmcxml: the XML entry as it appears in the data files available from the FTP site.
3. iprmctab: tab-delimited text version of the entry. Columns are the same as those in the text format returned by InterProScan.

Match/missmatch parameters (BLASTN only) are now supported by the NCBI BLAST webservice (Java and Perl clients only).

Many of the service WSDL documents (WSDL list) have been updated to change to the service endpoint. If you are using pre-generated stubs in your application these will need to be regenerated to use the service. The sample Java and C# clients (see services list) use pre-generated stubs and have been updated for the WSDL changes. Please see the clients page for the service of interest for an updated version of the client.

The WSPSIBlast web service is now available.

The WSDL for the PSI-Blast service (WSPSIBlast.wsdl) and a Perl WSPSIBlast client are now available. Please see the service and client pages for more details.

The WSPhobius web service is now available.

The WSPhobius WSDL (WSPhobius.wsdl) and a Perl WSPhobius client are also available. Please see the service and client pages for more details.

The WSPSISearch web service is now available.

The WSPSISearch WSDL (WSPSISearch.wsdl) and a Perl WSPSISearch client are also available. Please see the service and client pages for more details.

The WSMuscle service now uses the version 3.7 of muscle.

The MUSCLE WSDL (WSMuscle.wsdl) has been updated for a change to the service endpoint. If you are using pre-generated stubs in your application these will need to be regenerated to use the service.

Note: the Java WSMuscle client uses pre-generated stubs, please see the clients page for versions updated for this change.

The WSDbfetch service now supports multiple entry retrieval for the UniProtKB XML format.

The WSInterProScan WSDL (WSInterProScan.wsdl) has been updated for a change to the service endpoint. If you are using pre-generated stubs in your application these will need to be regenerated to use the service.

Note: the Java and .NET WSInterProScan clients use pre-generated stubs, please see the clients page for versions updated for this change.