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News (2011)

2012

News for 2012.

18th October 2011

The IPD-MHC protein and nucleotide datasets are now available for the SSS (FASTA, FASTM, NCBI BLAST, WU-BLAST, PSI-BLAST & PSI-Search) tools via REST & SOAP services:

  • IPD-MHC Nucleotide: ipdmhc
  • IPD-MHC Protein: ipdmhcp

For more details on IPD-MHC, see http://www.ebi.ac.uk/ipd/mhc/

Please note: One of our data centres will be offline from Friday 21st October 2011 at 14.00 (GMT+1) to Monday 24th October, 12 noon (GMT+1). Many of our web services will still be available during this period, as they will be run from the London data centres. However some services will be unavailable or have reduced functionality during this period.

26th September 2011

The Clustal Omega services ( REST & SOAP) have been updated to use Clustal Omega 1.0.3.

The PHI-BLAST functionality is supported in the PSI-BLAST services ( REST & SOAP).

20th September 2011

The WSPhobius service has been decommissioned, and replaced by:

The WSPhobius documentation has been archived and is provided solely for reference purposes:

7th September 2011

XML schema locations for sequence similarity search (SSS) and InterProScan results have been updated. The new locations are:

24th August 2011

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

The WSPhobius service will be decommissioned on Tuesday 20th September 2011. Users of WSPhobius should migrate to the replacement Phobius (REST) and/or Phobius (SOAP) services as soon as possible.

19th August 2011

Sequence and feature data from Ensembl Genomes is now available via the dbfetch services (dbfetch, WSDbfetch (REST) and WSDbfetch (SOAP)):

8th August 2011

The WSPhobius service has been deprecated. The decommissioning of the WSPhobius service is planned for Tuesday 20th September 2011 after which the service will no longer be available. Please migrate from WSPhobius to the replacement Phobius (REST) or Phobius (SOAP) services as soon as possible.

25th July 2011

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

29th June 2011

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

28th June 2011

A selection of sequence databases available in SRS@EBI and the dbfetch services (dbfetch, WSDbfetch (REST) & WSDbfetch (SOAP)) are now available in the generic sequence XML format: SeqXML, including:

  • EMBL-Bank
  • IMGT/HLA
  • IMGT/LIGM-DB
  • Patent Proteins
  • RefSeq
  • UniProtKB

See EBI Dbfetch Databases for a complete list.

24th June 2011

The multiple sequence alignment (MSA) selection of services has been expanded to include two new tools:

  1. DbClustal (DOI:10.1093/nar/28.15.2919; PMID:10908355): ClustalW based multiple sequence alignment from a protein BLAST result preserving aligned regions found by BLAST and using the full length sequences of the BLAST hits.
  2. MView (DOI:10.1093/bioinformatics/14.4.380; PMID:9632837): generate a multiple sequence alignment from a sequence similarity search result (e.g. from BLAST or FASTA) using the regions found by the sequence search. Can also be used to reformat and colour multiple sequence alignments.

Note: these services are in development and should currently be considered beta quality. Please report any issues found or suggestions for improvements to the services to EMBL-EBI Support.

20th June 2011

The FASTA and FASTM services have been updated to use FASTA 36.3.5a.

17th June 2011

The PDB data sources used by the dbfetch services (dbfetch, WSDbfetch (REST) and WSDbfetch (SOAP)) have been updated to include a source which takes into account the case sensitivity required to handle PDB chain sequence identifiers correctly (e.g. 3E3Q_A vs. 3E3Q_a), while still providing access to all the sequences for an entry (e.g. 3E3Q). Additionally the two commonly used styles of PDB chain sequence identifiers are supported: 3E3Q_A or 3E3QA.

The handling for the Protein Data Bank Markup Language (PDBML), aka. PDB XML, and macromolecular Crystallographic Information File (mmCIF) formats of the PDB has been extended to map PDB chain sequence identifiers to the corresponding structure entry so the hit identifiers from a sequence similarity search result can be used to get structure information in these formats, as well as in the PDB format.

1st June 2011

The IPD-MHC database of Major Histocompatibility Complex (MHC) sequences from a number of different species is available from the dbfetch services (dbfetch, WSDbfetch (REST) and WSDbfetch (SOAP)).

16th May 2011

Addition of annotsym parameter to the FASTA (REST) and FASTA (SOAP) services to allow annotation symbols contained in the sequence data (query and/or database) to be displayed on the alignments produced by FASTA.

Addition of a database of nucleotide sequences appearing in structures in the PDB (pdbna) to the sequence similarity search services:

10th May 2011

The scoreformat parameter has been added to the FASTM (REST) and FASTM (SOAP) services. This parameter provides access to the extended formats for the scores table in the FASTA output.

26th April 2011

The NCBI BLAST and PSI-BLAST services have been updated to use NCBI BLAST 2.2.25.

The following EMBOSS based services have been updated to use EMBOSS 6.3.1:

  • EMBOSS matcher
  • EMBOSS needle
  • EMBOSS stretcher
  • EMBOSS water

13th April 2011

The Align service has been retired and replaced with a collection of pairwise alignment services including the following tools:

29th March 2011

The documentation of the following discontinued services has been archived and the section referencing replacement services updated, in a effort to minimise confusion with the current services:

28th March 2011

The RPC/encoded SOAP multiple sequence alignment (MSA), sequence similarity search (SSS) and InterProScan services will be decommissioned today, Monday 28th March 2011. Details of the replacement REST and/or document/literal SOAP services, which should be used instead, can be found on the documentation pages for the old services:

28th February 2011

Web services for pairwise sequence alignment (comparison of two sequences), using a range of methods, are now available for testing:

24th February 2011

The RPC/encoded SOAP multiple sequence alignment (MSA) services will be decommissioned on Monday 28th March 2011. The replacement REST and/or document/literal SOAP services should be used instead. This effects the following services:

Details of the replacement services can be found on the documentation pages (above). All users should migrate to the new services as soon as possible.

22nd February 2011

The RPC/encoded SOAP sequence similarity search (SSS) services will be decommissioned on Monday 28th March 2011. The replacement REST and/or document/literal SOAP services should be used instead. This effects the following services:

All users should migrate to the new services as soon as possible.

21st February 2011

The FASTA services (FASTA (REST) and FASTA (SOAP)) have been updated to use FASTA 3.6. This update provides:

  1. multiple high-scoring alignments in the FASTA output, similar to the multiple HSPs in BLAST output. Currently this is disabled by default and can enabled using the hsps parameter.
  2. significant improvements to the performance of GGSEARCH and GLSEARCH allowing us to provide these methods for nucleotide database searching.
  3. control over the format of the scores table in the FASTA output. Using the scoreformat parameter additional information about the hits and alignments can be added to the scores table.
  4. bug fixes and performance improvements.

The FASTM services (FASTM (REST) and FASTM (SOAP)) have also been updated to use FASTA 3.6, and FASTM is now available for nucleotide searches as well as protein searches.

15th February 2011

The InterProScan RPC/encoded SOAP service (WSInterProScan) is now deprecated and no longer maintained. On Monday 28th March 2011 the service will be decommissioned. It is replaced by two new services:

All users should migrate to the new services as soon as possible.

25th January 2011

Services to create phylogentic trees from an existing multiple sequence alignment result are now available. The initial services are based on ClustalW:

Additional phylogeny services are to follow.

The ClustalW2 multiple sequence alignment services (ClustalW2 (REST) and ClustalW2 (SOAP)) have been updated to use ClustalW 2.1.

1st January 2011

Reminder

The following services have been replaced with new services and are no longer maintained and will be discontinued during 2011:

In addition the Protein Functional Analysis service WSInterProScan will be deprecated from the 15th February 2011 and will be decommissioned during 2011.

We recommend that all users of these services switch to the replacement services as soon as possible.

2010

 
about/news/2011.txt · Last modified: 2013/03/08 11:29 by hpm
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