Current

News for 2011.

The JDispatcher based InterProScan (REST) and InterProScan (SOAP) services have completed their beta preview phase and can now be considered production services. As part of the transition between the old and new services, the Dispatcher based WSInterProScan service will be deprecated from the 15th February 2011 and will be decommissioned later in 2011. We recommend that used of the WSInterProScan web service begin migrating their usage to the new services as soon as possible.

Sample Java client using the JAX-WS RI SOAP tool-kit, included in Java 6, is now available for InterProScan (SOAP).

The HGNC, IMGT/HLA, IMGT/LIGM-DB and IPD-KIR databases have been added to the dbfetch services:

• dbfetch
• WSDbfetch
• WSDbfetch (REST)

Please Note: Due to essential system maintenance some services will be unavailable on Tuesday 7th December 2010 between 09:30 AM and 12:30 PM GMT. Apologies for any inconvenience caused.

While the RPC/encoded SOAP services for InterProScan, Sequence Similarity Search (SSS) and Multiple Sequence Alignment (MSA) will be affected by this downtime, the equivalent REST and document/literal SOAP services will not be affected. Please see the documentation for these services for further information:

• Multiple Sequence Alignment (MSA)
  • ClustalW2 (REST)
  • ClustalW2 (SOAP)
  • Kalign (REST)
  • Kalign (SOAP)
  • MAFFT (REST)
  • MAFFT (SOAP)
  • MUSCLE (REST)
  • MUSCLE (SOAP)
  • PRANK (REST)
  • PRANK (SOAP)
  • T-COFFEE (REST)
  • T-COFFEE (SOAP)
• Protein Functional Analysis (PFA)
  • InterProScan (REST)
  • InterProScan (SOAP)
• Sequence Similarity Search (SSS)
  • FASTA (REST)
  • FASTA (SOAP)
  • FASTM (REST)
  • FASTM (SOAP)
  • NCBI BLAST (REST)
  • NCBI BLAST (SOAP)
  • PSI-BLAST (REST)
  • PSI-BLAST (SOAP)
  • PSI-Search (REST)
  • PSI-Search (SOAP)
  • WU-BLAST (REST)
  • WU-BLAST (SOAP)

Due to a fault in the Hintxon data centre services were unavailable between 15:00 and 18:00 GMT. The fault has been addressed and we are working to restore normal service. Apologies for any inconvenience caused.

The RESID and Taxonomy databases have been added to the dbfetch services:

• dbfetch
• WSDbfetch
• WSDbfetch (REST)

Our existing similarity and homology search services have been migrated to a new data centre and the older versions of these services have now been deprecated. For more information, please have a look at the following page or contact EBI support.

The dbfetch web services have been updated providing:

1. Additional functionality
   • Option to suppress EMBL-EBI HTML header and footer (see dbfetch).
   • OBDA biofetch compatibility (see dbfetch).
   • Support for format and database aliases (e.g. using swissprot to access uniprotkb).
   • Meta-information methods for REST service (see WSDbfetch (REST)).
   • Detailed meta-information for SOAP service (see WSDbfetch (SOAP)).
2. New databases
   • EMBLCONEXP (emblconexp).
   • Patent DNA NRL1 (nrnl1).
   • Patent DNA NRL2 (nrnl2).
   • Patent Protein NRL1 (nrpl1).
   • Patent Protein NRL2 (nrpl2).
   • Trace Archive (tracearchive).
3. Additional formats:
   • annot for all sequence databases where annotation and sequence can be separated.
   • entrysize for all sequence databases where the source database can provide information about the entry size.
   • emblxml-1.2 for EMBL-Bank databases (e.g. embl, emblcds, emblcon, etc.).
   • mmcif and pdbml for PDB.

• The proteomes, genomes and wgs databases available in the FASTA services (FASTA, FASTA (REST) and FASTA (SOAP)) have been updated to their latest version.
• The T-COFFEE services (T-COFFEE, T-COFFEE (REST) and T-COFFEE (SOAP)) have been updated to use version 8.9.3 of the program
• The MUSCLE services (MUSCLE, MUSCLE (REST) and MUSCLE (SOAP)) can now generate log and tree output files
• SGT results now have hyperlinks to their corresponding entry in the TargetDB website
• New services for peptide fragment searches (FASTM, FASTM (REST) and FASTM (SOAP)) are now available in beta version.

The FASTA services: FASTA (REST) and FASTA (SOAP), have been modified to remove the program options for fastf, fastm and fasts. This is due to an input incompatibility between these programs and the other FASTA programs. The peptide fragment searches provided by fastf, fastm and fasts are still available in WSFasta and are to be re-introduced in a separate service (FASTM) in the near future.

The following RPC/encoded SOAP services are now deprecated and no longer maintained:

• Sequence Similarity Search
  • WSFasta
  • WSNCBIBlast
  • WSPSIBlast
  • WSPSISearch
  • WSWUBlast
• Multiple Sequence Alignment
  • WSClustalW2
  • WSKalign
  • WSMafft
  • WSMuscle
  • WSTCoffee

Please use the equivalent REST or document/literal SOAP service (see Web Services).

REST and SOAP Web Services for the PRANK multiple sequence alignment method are now available, see the following for details:

• PRANK (REST)
• PRANK (SOAP)

The WSDbfetch (SOAP) service now provides a document/literal interface in addition to the RPC/encoded interfaces.

Sample clients for the new interface are provided for Java, Perl and Python.

.NET clients are now available for the following sequence similarity search (SSS) services:

• PSI-BLAST (SOAP)
• PSI-Search (SOAP)

A Perl client is now available for the PSI-Search (SOAP) service.

The following services have been updated to use FASTA 35.4.10:

• FASTA (REST)
• FASTA (SOAP)
• PSI-Search (REST)
• PSI-Search (SOAP)
• WSFasta
• WSPSISearch

.NET clients are now available for the following multiple sequence alignment (MSA) services:

• ClustalW2 (SOAP)
• Kalign (SOAP)
• MAFFT (SOAP)
• MUSCLE (SOAP)
• T-Coffee (SOAP)

The WSMPsrch and WSScanPS services have been retired.

For equivalent functionality please use SSEARCH (FASTA (REST), FASTA (SOAP) or WSFasta) or PSI-Search (PSI-Search (REST), PSI-Search (SOAP) or WSPSISearch).

Updated sample clients are now available for the EB-eye service:

• Java client using Axis
• Java client using JAX-WS
• Perl client SOAP::Lite

Users are advised to use the latest release of the available EB-eye clients to deal properly with forthcoming version of the implementation on the server side.

Reminder: the hands-on course ”Programmatic Access To Biological Databases (Perl)” will be held on 22nd–26th February 2010 at the European Bioinformatics Institute. The registration deadline is Thursday 21st January 2010, see the Hands-on training at EBI pages for details of how to register.

News for 2009.