As previously announce the WSEmboss service has been decommissioned. For alternative EMBOSS services please see the Soaplab page.

As previously announced the International Protein Index (IPI) databases (IPI and IPI History) have been removed from dbfetch, WSDbfetch and SRS@EMBL-EBI.

Replacement data is available from UniProt (see http://www.uniprot.org/news/2011/06/28/release and http://www.uniprot.org/taxonomy/complete-proteomes). The underlying data for IPI has been archived and is available from the EMBL-EBI FTP site under ftp://ftp.ebi.ac.uk/pub/databases/IPI/.

Users wishing to convert annotations using IPI identifiers in to their equivalents using UniProt identifiers (UniProtKB or UniParc) may find the following services helpful:

• UniProt.org Database identifier mapping (REST service).
• Protein Identifier Cross-Reference (PICR) (SOAP service or REST service).

The new web services for FingerPRINTScan, Pratt and PROSITE Scan are available to the public:

• FingerPRINTScan (REST)
• FingerPRINTScan (SOAP)
• Pratt (REST)
• Pratt (SOAP)
• PROSTIE Scan (REST)
• PROSTIE Scan (SOAP)

The final release of the International Protein Index (IPI) database was produced in 2011, and has been replaced by equivalent data available from UniProt (see http://www.uniprot.org/news/2011/06/28/release and http://www.uniprot.org/taxonomy/complete-proteomes).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 The underlying data has been archived and will remain available from the EMBL-EBI FTP site under ftp://ftp.ebi.ac.uk/pub/databases/IPI/.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 The data for Genome Reviews, which was used by these servcices, has been archived and remains available from the EMBL-EBI FTP site under ftp://ftp.ebi.ac.uk/pub/databases/genome_reviews/ and ftp://ftp.ebi.ac.uk/pub/databases/integr8/.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.

Archived news for 2012.