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News (2013)

2014

News for 2014.

Thursday 19th December 2013

The EMBL-EBI SRS service has been retired. Users should see the EMBL-EBI Services and EMBL-EBI Web Services pages for alternative ways to access databases available from EMBL-EBI, and the SRS@EMBL-EBI Service Retirement page for details of other sites providing access to databanks and tools which have been provided in SRS@EMBL-EBI.

Monday 16th December 2013

The RESID database has been retired from the EB-eye search engine. More information about the RESID Database of Protein Modifications can be found at http://pir.georgetown.edu/resid/.

Tuesday 3rd December 2013

The InterProScan 5 services (InterProScan 5 (REST) & InterProScan 5 (SOAP)) have been updated to use InterProScan v5.3-45.0.

Thursday 14th November 2013

The FASTA services (FASTA (REST) & FASTA (SOAP)), the FASTM services (FASTM (REST) & FASTM (SOAP)) and the lalign (lalign (REST) & lalign (SOAP)) services have been updated to use FASTA version 36.3.6d (Nov, 2013).

Tuesday 22th October 2013

The FASTA services (FASTA (REST) & FASTA (SOAP)) and the FASTM services (FASTM (REST) & FASTM (SOAP)) have been updated to use FASTA version 36.3.6d.

Thursday 17th October 2013

The InterProScan 5 services (InterProScan 5 (REST) & InterProScan 5 (SOAP)) have been updated to inclued the application Coils.

Thursday 10th October 2013

The EMBL-EBI SRS service will be retired on Thursday 19th December 2013. Please see the main EMBL-EBI site (http://www.ebi.ac.uk/services/) for alternative ways to access databases available from EMBL-EBI, and the Discontinued Databanks and Tools page for details of other sites providing access to databanks and tools which have been provided by SRS@EMBL-EBI.

Tuesday 8th October 2013

The InterProScan 5 services (InterProScan 5 (REST) & InterProScan 5 (SOAP)) have been updated to use InterProScan v5-44.0.

Monday 30th September 2013

The MView services (MView (REST) & MView (SOAP)) have been updated to use MView v1.54.

Thursday 29th August 2013

The FASTA services (FASTA (REST) & FASTA (SOAP)) have been updated to use FASTA version 36.3.6c.

Wednesday 14th August 2013

Tuesday 9th July 2013

The following services have been updated to use FASTA version 36.3.6.

- The FASTA services (FASTA (REST) & FASTA (SOAP))
- The FASTM services (FASTM (REST) & FASTM (SOAP)) &
- The lalign services (lalign (REST) & lalign (SOAP)).

Wednesday 26th June 2013

The Clustal Omega services (Clustal Omega (REST) & Clustal Omega (SOAP)) have been updated to use Clustal Omega version 1.2.0.

Monday 10th June 2013

The Clustal Omega services (Clustal Omega (REST) & Clustal Omega (SOAP)) have been updated to use Clustal Omega version 1.1.1.

Wednesday 29th May 2013

The HGVbase database has been retired from the Sequence Similarity Search (SSS) services. To continue access to the relevant data, please visit

- GWAS Central: https://www.gwascentral.org/
- 1000 Genomes: http://www.1000genomes.org/
- DGVa : http://www.ebi.ac.uk/dgva/
- Ensembl: http://www.ensembl.org/
- EGA: http://www.ebi.ac.uk/ega/
- LRG: http://www.lrg-sequence.org/
- NCBI dbSNP: http://www.ncbi.nlm.nih.gov/SNP/
- Archived data on the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/hgbase/

Tuesday 21st May 2013

A neighbour-joining phylogenetic tree and a percentage identity matrix (PIM) are available from the web services of Clustal Omega, ClustalW2, Kalign, MAFFT, MUSCLE and T-Coffee.

Tuesday 15th May 2013

The HGVbase database will be retired from the Sequence Similarity Search (SSS) services on Wednesday 29/05/2013.

To continue access to the relevant data, please visit
- GWAS Central: https://www.gwascentral.org/
- 1000 Genomes: http://www.1000genomes.org/
- DGVa : http://www.ebi.ac.uk/dgva/
- Ensembl: http://www.ensembl.org/
- EGA: http://www.ebi.ac.uk/ega/
- LRG: http://www.lrg-sequence.org/
- NCBI dbSNP: http://www.ncbi.nlm.nih.gov/SNP/
- Archived data on the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/hgbase/

Wednesday 17th April 2013

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

Monday 15th April 2013

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:

18th March 2013

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

8th March 2013

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/.

4th March 2013

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/.

25th February 2013

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.

20th February 2013

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

15th February 2013

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/.

13th February 2013

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.

11th February 2013

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.

1st February 2013

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

2012

Archived news for 2012.

 
about/news/2013.txt · Last modified: 2014/03/05 10:37 by hpm
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