about:news [2013/03/18 16:43]
wli (172.22.69.114) |
about:news [2013/08/29 11:02] (current)
wli (172.22.69.249) |
| | ====== News ====== | | ====== News ====== |
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| | + | ==== Thursday 29th August 2013 ==== |
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| | + | The FASTA services ([[services:sss:fasta_rest|FASTA (REST)]] & [[services:sss:fasta_soap|FASTA (SOAP)]]) have been updated to use FASTA version 36.3.6c. |
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| | + | ==== Wednesday 14th August 2013 ==== |
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| | + | The FASTA services ([[services:sss:fasta_rest|FASTA (REST)]] & [[services:sss:fasta_soap|FASTA (SOAP)]]) have been updated to use FASTA version 36.3.6b. |
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| | + | The PROSITE Scan services ([[:services:pfa:ps_scan_rest|PROSITE Scan (REST)]] & [[:services:pfa:ps_scan_soap|PROSITE Scan (SOAP)]]) have been updated to use ps_scan-1.79.1. |
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| | + | The following EMBOSS tools services have been updated to use EMBOSS-6.6.0: |
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| | + | - [[:services:psa:EMBOSS matcher (REST)]] & [[:services:psa:EMBOSS matcher (SOAP)]] \\ |
| | + | - [[:services:psa:EMBOSS needle (REST)]] & [[:services:psa:EMBOSS needle (SOAP)]] \\ |
| | + | - [[:services:psa:EMBOSS stretcher (REST)]] & [[:services:psa:EMBOSS stretcher (SOAP)]] \\ |
| | + | - [[:services:psa:EMBOSS water (REST)]] & [[:services:psa:EMBOSS water (SOAP)]] \\ |
| | + | - [[:services:sfc:EMBOSS seqret (REST)]] & [[:services:sfc:EMBOSS seqret (SOAP)]] \\ |
| | + | - [[:services:seqstats:EMBOSS cpgplot (REST)]] & [[:services:seqstats:EMBOSS cpgplot (SOAP)]] \\ |
| | + | - [[:services:seqstats:EMBOSS newcpgreport (REST)]] & [[:services:seqstats:EMBOSS newcpgreport (SOAP)]] \\ |
| | + | - [[:services:seqstats:EMBOSS isochore (REST)]] & [[:services:seqstats:EMBOSS isochore (SOAP)]] \\ |
| | + | - [[:services:seqstats:EMBOSS pepinfo (REST)]] & [[:services:seqstats:EMBOSS pepinfo (SOAP)]] \\ |
| | + | - [[:services:seqstats:EMBOSS pepstats (REST)]] & [[:services:seqstats:EMBOSS pepstats (SOAP)]] \\ |
| | + | - [[:services:seqstats:EMBOSS pepwindow (REST)]] & [[:services:seqstats:EMBOSS pepwindow (SOAP)]]\\ |
| | + | - [[:services:st:EMBOSS transeq (REST)]] & [[:services:st:EMBOSS transeq (SOAP)]] \\ |
| | + | - [[:services:st:EMBOSS sixpack (REST)]] & [[:services:st:EMBOSS sixpack (SOAP)]] \\ |
| | + | - [[:services:st:EMBOSS backtranseq (REST)]] & [[:services:st:EMBOSS backtranseq (SOAP)]] \\ |
| | + | - [[:services:st:EMBOSS backtranambig (REST)]] & [[:services:st:EMBOSS backtranambig (SOAP)]] \\ |
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| | + | ==== Tuesday 9th July 2013 ==== |
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| | + | The following services have been updated to use FASTA version 36.3.6. |
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| | + | - The FASTA services ([[services:sss:fasta_rest|FASTA (REST)]] & [[services:sss:fasta_soap|FASTA (SOAP)]]) \\ |
| | + | - The FASTM services ([[services:sss:fastm_rest|FASTM (REST)]] & [[services:sss:fastm_soap|FASTM (SOAP)]]) & \\ |
| | + | - The lalign services ([[services:psa:lalign_rest|lalign (REST)]] & [[services:psa:lalign_soap|lalign (SOAP)]]). \\ |
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| | + | ==== Wednesday 26th June 2013 ==== |
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| | + | The Clustal Omega services ([[services:msa:clustalo_rest|Clustal Omega (REST)]] & [[services:msa:clustalo_soap|Clustal Omega (SOAP)]]) have been updated to use Clustal Omega version 1.2.0. |
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| | + | ==== Monday 10th June 2013 ==== |
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| | + | The Clustal Omega services ([[services:msa:clustalo_rest|Clustal Omega (REST)]] & [[services:msa:clustalo_soap|Clustal Omega (SOAP)]]) have been updated to use Clustal Omega version 1.1.1. |
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| | + | ==== Wednesday 29th May 2013 ==== |
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| | + | 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/ \\ |
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| | + | ==== Tuesday 21st May 2013 ==== |
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| | + | A neighbour-joining phylogenetic tree and a percentage identity matrix (PIM) are available from the web services of [[:services:msa:clustalo_soap|Clustal Omega]], [[:services:msa:clustalw2_soap|ClustalW2]], [[:services:msa:kalign_soap|Kalign]], [[:services:msa:mafft_soap|MAFFT]], [[:services:msa:muscle_soap|MUSCLE]] and [[:services:msa:tcoffee_soap|T-Coffee]]. |
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| | + | ==== Tuesday 15th May 2013 ==== |
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| | + | The HGVbase database will be retired from the Sequence Similarity Search (SSS) services on Wednesday 29/05/2013. |
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| | + | 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/ \\ |
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| | + | ==== Wednesday 17th April 2013 ==== |
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| | + | As previously announced the [[:services:archive:so:WSEmboss]] service has been decommissioned. For details of alternative EMBOSS services please see the [[:services:archive:soaplab:overview|Soaplab]] page. |
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| | + | ==== Monday 15th April 2013 ==== |
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| | + | As previously announced the International Protein Index (IPI) databases (IPI and IPI History) have been removed from [[http://www.ebi.ac.uk/Tools/dbfetch/|dbfetch]], [[:services:dbfetch|WSDbfetch]] and [[http://srs.ebi.ac.uk/|SRS@EMBL-EBI]]. |
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| | + | 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 [[ftp://ftp.ebi.ac.uk/|EMBL-EBI FTP site]] under [[ftp://ftp.ebi.ac.uk/pub/databases/IPI/]]. |
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| | + | Users wishing to convert annotations using IPI identifiers in to their equivalents using UniProt identifiers (UniProtKB or UniParc) may find the following services helpful: |
| | + | * [[http://www.uniprot.org/?tab=mapping|UniProt.org Database identifier mapping]] ([[http://www.uniprot.org/faq/28#id_mapping_examples|REST service]]). |
| | + | * [[http://www.ebi.ac.uk/Tools/picr/|Protein Identifier Cross-Reference (PICR)]] ([[http://www.ebi.ac.uk/Tools/picr/WSDLDocumentation.do|SOAP service]] or [[http://www.ebi.ac.uk/Tools/picr/RESTDocumentation.do|REST service]]). |
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| | ==== 18th March 2013 ==== | | ==== 18th March 2013 ==== |
| | * [[:services:pfa:Pratt (REST)]] | | * [[:services:pfa:Pratt (REST)]] |
| | * [[:services:pfa:Pratt (SOAP)]] | | * [[:services:pfa:Pratt (SOAP)]] |
| - | * [[:services:pfa:ps_scan_rest|PROSTIE Scan (REST)]] | + | * [[:services:pfa:ps_scan_rest|PROSITE Scan (REST)]] |
| - | * [[:services:pfa:ps_scan_soap|PROSTIE Scan (SOAP)]] | + | * [[:services:pfa:ps_scan_soap|PROSITE Scan (SOAP)]] |
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| | ==== 8th March 2013 ==== | | ==== 8th March 2013 ==== |
