Current

News for 2010.

As detailed in the EMBL-Bank Forthcoming Changes entries in the ANN data class in EMBL-Bank will be migrated into the CON data class in the next release (102; Dec 2009). Thus the emblann database in WSDbfetch (SOAP and REST) will no longer be available once the release becomes available.

Queries which used emblann as the database will need to use emblcon or embl to get the equivalent data.

REST and SOAP document/literal services for sequence similarity search and multiple sequence alignment are now available, see the following pages for details of the services:

• REST
  • FASTA (REST)
  • NCBI BLAST (REST)
  • PSI-BLAST (REST)
  • PSI-Search (REST)
  • WU-BLAST (REST)
• SOAP document/literal
  • FASTA (SOAP)
  • NCBI BLAST (SOAP)
  • PSI-BLAST (SOAP)
  • PSI-Search (SOAP)
  • WU-BLAST (SOAP)

Note: the SOAP RPC/encoded services will be phased out in favor of the SOAP document/literal services over the next year, so we encourage developers to evaluate the new services, and begin migration of their usage as soon as possible.

WSDbfetch (SOAP and REST) has been updated to provide two generic formats for the major sequence databases:

1. annot: returns the annotation in the default format, the sequence is not included.
2. entrysize: returns a tab delimited table describing the size of the entry. The four fields are:
   1. entry identifier (in DB:ID format)
   2. size of the annotation (bytes)
   3. length of the sequence (nt or aa)
   4. an estimate of the whole entry size (annotation size + sequence length)

These formats provide a mechanism to control the amount of data retrieved for an entry, this is important when dealing with databases which can contain very large entries (e.g. EMBL-Bank and RefSeq).

WSClustalW2 has been updated to use ClustalW 2.0.12.

With the release of Ensembl release 56 WSDbfetch (SOAP and REST) support for Ensembl Gene (ensemblgene) has been extended to restore support for the following formats: EMBL, GenBank, CSV, tab delimited, GFF and GFF 3.

WSNCBIBlast has been updated to use NCBI BLAST 2.2.21.

WSTCoffee has been updated to use T-Coffee 8.06.

C#, Java and Perl sample clients are now available for the EB-eye service. See the service page for more details.

REST web services for QuickGO, an interface to the Gene Ontology (GO) and Gene Ontology Annotation (GOA) databases, are now available.

Sample Perl client using SOAP::Lite is now available for the EB-eye web service.

WSClustalW2 has been updated to use ClustalW 2.0.11.

WSFasta has been updated to use FASTA 35.4.8.

WSNCBIBlast has been updated to use NCBI BLAST 2.2.20.

The WSInterProScan service now uses the faster and more accurate PatternScan method, by default, to perform PROSITE pattern searches. The older ScanRegEx method can be used by specifying it in the list of methods to be performed.

In most cases the only difference in the output is the replacement of the “ScanRegEx” method name with “PatternScan” for PROSITE pattern matches. If your are parsing the output and explicitly search for the ScanRegEx name you will need to update your parser to allow for the change in method name.

If you have comments or feedback regarding InterProScan, please let us know by using the feedback form.

The WSDaliLite service has been changed to return a ZIP archive containing all the files generated by the program, rather then just the HTML index page. If you want the service to be able to return individual files please contact us providing details of the relevant use case.

WSInterProScan and WSWUBlast documentation updated for the addition of service methods to get parameter information from the service. The C#, Java and Perl, WSInterProScan and WSWUBlast have been updated to provide options to access this additional information.

WSFasta has been updated to use FASTA 35.4.6.

The WSDbfetch (SOAP and REST) services have been updated to provide six new citation formats for MEDLINE entries. These are:

1. bibtex: BibTeX
2. endnote: EndNote text format
3. isi: ISI format, as used in ISI Web of Knowledge
4. modsxml: MODS XML
5. ris: RIS, as used by Reference Manager and ProCite
6. wordbibxml: MS Word bibliography XML (see http://mahbub.wordpress.com/2007/03/22/deciphering-microsoft-office-2007-bibliography-format/)

These formats are provided using bibutils, a set of open source tools for bibliography format interconversion.

Advance notice: on 3rd March 2009 the database prefixes used in BLAST and FASTA results for the UniProtKB data will be changed to from “SW” to “SP” for UniProtKB/SwissProt and from “TREMBL” to “TR” for UniProtKB/TrEMBL. Searches against the whole of UniProtKB will return a mixture of these prefixes, indicating which entries come from the human curated section of the database.

The MSD group has changed its name to the PDBe to reflect is close partnership with the wwPDB project. This change is also taken into account by the EB-eye:the domain name has been changed from 'msd' to 'pdbe'.

Due to hardware changes at EBI the SignalP method in the InterProScan service is currently failing. The problem is being investigated and we hope to have a fix in place soon. In the meantime we suggest running without the SignalP method.

Update: the SignalP method in the InterProScan service is now working again.

News for 2008.