The final release of the International Protein Index (IPI) database was produced in 2011, and has been replaced by equivalent data available from UniProt (see http://www.uniprot.org/news/2011/06/28/release and http://www.uniprot.org/taxonomy/complete-proteomes). To allow users to transition from Genome Reviews to the new resources the IPI data has continued to be available in dbfetch, WSDbfetch and SRS@EMBL-EBI. On Monday 15th April 2013 the IPI databases will be removed from the dbfetch, WSDbfetch and SRS@EMBL-EBI services. The underlying data has been archived and will remain available from the EMBL-EBI FTP site under ftp://ftp.ebi.ac.uk/pub/databases/IPI/.

The International Protein Index (IPI) database is retired from the Sequence Similarity Search (FASTA, FASTM, NCBI BLAST, PSI-BLAST, PSI-Search & WU-BLAST). Equivalent data is available from UniProt (see http://www.uniprot.org/news/2011/06/28/release and http://www.uniprot.org/taxonomy/complete-proteomes). For queries relating to this database retirement please contact us via EMBL-EBI Support.

The Genome Reviews databases which were available in dbfetch, WSDbfetch and SRS@EMBL-EBI, have now been retired. The data for Genome Reviews, which was used by these servcices, has been archived and remains available from the EMBL-EBI FTP site under ftp://ftp.ebi.ac.uk/pub/databases/genome_reviews/ and ftp://ftp.ebi.ac.uk/pub/databases/integr8/.

The FASTA service against proteomes is retired. To continue accessing the complete proteome data, please visit UniProt Complete and Reference Proteomes, Ensembl, Ensembl Genomes or use the WU-BLAST web service to search the Ensembl Genomes sequence databases. For queries relating to this data retirement please contact us via EMBL-EBI Support.

The WSCensor service has been retired. The replacement services: CENSOR (REST) and CENSOR (SOAP) should be used instead.

The final releases of the Genome Reviews databases were produced in 2011, and have been replaced by data available from Ensembl and Ensembl Genomes. To allow users to transition from Genome Reviews to the new resources the Genome Reviews data has continued to be available in dbfetch, WSDbfetch and SRS@EMBL-EBI. On Monday 4th March 2013 the Genome Reviews, Genome Reviews Gene Sets and Genome Reviews Transcript Sets databases will be removed from the dbfetch, WSDbfetch and SRS@EMBL-EBI services. The underlying data has been archived and will remain available from the EMBL-EBI FTP site under ftp://ftp.ebi.ac.uk/pub/databases/genome_reviews/ and ftp://ftp.ebi.ac.uk/pub/databases/integr8/.

The International Protein Index (IPI) database will be retired from the Sequence Similarity Search (FASTA, FASTM, NCBI BLAST, PSI-BLAST, PSI-Search & WU-BLAST) services on 27/02/2013. Equivalent data is available from UniProt (see http://www.uniprot.org/news/2011/06/28/release and http://www.uniprot.org/taxonomy/complete-proteomes). For queries relating to this database retirement please contact us via EMBL-EBI Support.

The FASTA service against proteomes will be retired on 25/02/2013. To continue accessing the complete proteome data, please visit UniProt Complete and Reference Proteomes, Ensembl, Ensembl Genomes or use the WU-BLAST web service to search the Ensembl Genomes sequence databases. For queries relating to this data retirement please contact us via EMBL-EBI Support.

The EMBL-EBI Soaplab server has been decommissioned. The Soaplab documentation has been updated to provide details of alternative services.

New web services for CENSOR are now available:

• CENSOR (REST)
• CENSOR (SOAP)

The old WSCensor service has been deprecated and should not be used for new development.

The WSDaliLite and WSMaxsprout services have been decommissioned, and replaced by:

• DaliLite:
  • DaliLite (REST)
  • DaliLite (SOAP)
• MaxSprout:
  • MaxSprout (REST)
  • MaxSprout (SOAP)

The documentation for the WSDaliLite and WSMaxsprout services has been archived and is provided for reference purposes:

• DaliLite:
  • WSDaliLite
  • WSDaliLite clients
• MaxSprout:
  • WSMaxsprout
  • WSMaxsprout clients

The FASTA (REST & SOAP), FASTM (REST & SOAP) and lalign (REST & SOAP) services have been updated to use FASTA version 36.3.5e Sep, 2012(preload8).

As previously mentioned the old CiteXplore v1 web service will be retired on the 31st October 2012. Users should migrate all usage to the replacement CiteXplore v3.0.1 web service as soon as possible. For queries relating to this service retirement please contact us via. EMBL-EBI Support.

The new web services for DaliLite and MaxSprout have come out of beta:

• DaliLite (REST)
• DaliLite (SOAP)
• MaxSprout (REST)
• MaxSprout (SOAP)

The old WSDaliLite and WSMaxsprout services have been deprecated and will be decommissioned on Tuesday 27th November 2012.

A set of services for sequence format conversion and now available for beta testing:

• EMBOSS seqret (REST)
• EMBOSS seqret (SOAP)
• Readseq (REST)
• Readseq (SOAP)

These services focus on the format conversion and manipulation of sequence data, for a tool specialising in the manipulation and format conversion of multiple sequence alignment formats, see MView (REST or SOAP).

New web services for DaliLite and MaxSprout are now available for beta testing:

• DaliLite (REST)
• DaliLite (SOAP)
• MaxSprout (REST)
• MaxSprout (SOAP)

Please report any feedback or issues encountered to us via. EMBL-EBI Support.

REST and SOAP (document/literal) Web Services of PromoterWise for pair-wise alignments are now available, see the following for details:

• PromoterWise (REST)
• PromoterWise (SOAP)

REST and SOAP (document/literal) Web Services of GeneWise & Wise2DBA for pair-wise alignments are now available, see the following for details:

• GeneWise (REST)
• GeneWise (SOAP)
• Wise2DBA (REST)
• Wise2DBA (SOAP)

Recently a new version of the CiteXplore Web Service was released by the Literature Services Group.

The latest Web Service (version 3.0.1) is SOAP based and gives programmatic access to all of the publications and related information in UK PubMed Central. An example Java client is provided, together with comprehensive documentation on the new methods available. Version 3 of the service has been modularised, and allows users to pick and choose the components required, making information retrieval more efficient.

The new Web Service is now also being used by the front-end application of UK PubMed Central, improving its performance. Version 1 of the Web Service will be maintained for use until the end of October 2012.

The FASTA ( REST & SOAP), FASTM ( REST & SOAP) and lalign ( REST & SOAP) services have been updated to use FASTA version 36.3.5c Jun, 2012(preload8).

REST and SOAP (document/literal) Web Services for SAPS, EMBOSS pepinfo, pepstats and pepwindow are now available, see the following for details:

• EMBOSS pepinfo (REST)
• EMBOSS pepinfo (SOAP)
• EMBOSS pepstats (REST)
• EMBOSS pepstats (SOAP)
• EMBOSS pepwindow (REST)
• EMBOSS pepwindow (SOAP)
• SAPS (REST)
• SAPS (SOAP)

The NCBI BLAST services ( REST & SOAP) have been updated to use NCBI BLAST 2.2.26.

The Clustal Omega services ( REST & SOAP) have been updated to use Clustal Omega 1.1.0 and nucleotide alignments are now supported.

The EBI Application Result XML contents for sequence similarity search have been updated with alignment strand information in a consistent format (e.g. <strand>minus/plus</strand> means the query is “minus” (“reverse”) and the subject is “plus” (“forward”)).

REST and SOAP (document/literal) Web Services for EMBOSS translation tools are now available, see the following for details:

• EMBOSS Transeq (REST)
• EMBOSS Transeq (SOAP)
• EMBOSS Sixpack (REST)
• EMBOSS Sixpack (SOAP)
• EMBOSS Backtranseq (REST)
• EMBOSS Backtranseq (SOAP)
• EMBOSS Backtranambig (REST)
• EMBOSS Backtranambig (SOAP)

The dbfetch services (dbfetch, WSDbfetch (REST) and WSDbfetch (SOAP)) have been updated to include summary information detailing the data sources used by dbfetch in the database meta-information.

Archived news for 2011.