Changelog

Version 2.33, February 2019

  • Changes
    • UniProtKB release 2019_02
    • Ensembl Genomes release 42
    • Ensembl release 95
  • Bug fixes
    • Fix to ‘Taxonomy Search’ and ‘Accession Search’ forms
  • New features
    • Added query alignment/HMM to ‘Search Details’ (previously the query was only shown for fasta input), and taxonomic IDs if selected; HMMs and alignments are truncated but the full input is available via a new /query endpoint

Version 2.32, January 2019

  • Changes
    • UniProtKB release 2019_01

Version 2.31, December 2018

  • Changes
    • UniProtKB release 2018_11

Version 2.30, November 2018

  • Changes
    • UniProtKB release 2018_10
    • Ensembl Genomes release 41
    • Ensembl release 94
  • New features
    • Added phylum as an optional column in the results table

Version 2.29, October 2018

  • Changes
    • UniProtKB release 2018_09

Version 2.28, September 2018

  • Changes
    • Pfam release 32.0
  • Bug fixes
    • Fix to display of position in queue for batch searches

Version 2.27, September 2018

  • Changes
    • UniProtKB release 2018_08

Version 2.26, August 2018

  • Changes
    • Ensembl Genomes release 40
    • Ensembl release 93
    • ChEMBL added as a supported sequence database (version 24)
  • Bug fixes
    • Fix to searches against TreeFam using the API (prior to this, searches used the gathering threshold, which does not apply to this database)

Version 2.25, July 2018

  • Changes
    • UniProt release 2018_07

Version 2.24, June 2018

  • Changes
    • UniProt release 2018_06
  • New features
    • Added new “fisheye” mode on the taxonomy viewer

Version 2.23, May 2018

  • Changes
    • UniProt release 2018_05
    • Ensembl Genomes release 39
    • Ensembl release 92
  • Bug fixes
    • Improvements to the taxonomy page performance

Version 2.22, April 2018

  • Changes
    • UniProt release 2018_04
    • Introduced TreeFam, version 9, with post-processing using the default TreeFam e-value threshold and hit selection
    • Website annotated using Schemas.org and current working version of BioSchemas

Version 2.21, January 2018

  • Changes
    • UniProt release 2018_01
    • Ensembl Genomes release 38

Version 2.20, December 2017

  • Changes
    • UniProt release 2017_12
    • Ensembl release 91

Version 2.19, November 2017

  • Changes
    • UniProt release 2017_11
    • MEROPS 12

Version 2.18, October 2017

  • Changes
    • UniProt release 2017_10
    • Gene3D version 16.0.0
  • Bug fixes
    • Fix XML output for some API endpoints

Version 2.17, September 2017

  • Changes
    • UniProt release 2017_09
    • Ensembl Genomes release 37
    • Ensembl release 90
  • New features

Version 2.16, August 2017

  • Changes
    • UniProt release 2017_08
    • Change some email templates to have tab-delimited headers and rows
  • New features
    • Added information warning about next release across the website

Version 2.15, July 2017

  • Changes
    • UniProt release 2017_07
    • Ensembl Genomes release 36
    • Ensembl release 89
    • New option “unselect all” for jackhmmer iterations
    • New endpoints available as JSON (taxonomy and domain architecture)
  • Bug fixes
    • Download of ClustalW, PSI-BLAST and PHYLIP file formats fixed

Version 2.14, June 2017

  • Changes
    • UniProt release 2017_06

Version 2.13, May 2017

  • Changes
    • UniProt release 2017_05
    • Ensembl Genomes release 35
    • Ensembl release 88
    • Gene3D post-processing now uses cath-resolve-hits

Version 2.12

  • Changes
    • Website now follows EBI guidelines
    • EBI Search cross-references added for all supported databases

Version 2.11, March 2017

  • Changes
    • UniProt release 2017_03
    • Pfam release 31.0
    • MEROPS 11 added as a supported sequence database
    • PIRSF: new post-processing enables the unification of two or more matches that are separated due to the HMMER3 local-local matching model
    • (beta version) Added EBI Search cross-references in sequence database results

Version 2.10, February 2017

  • Changes
    • UniProt release 2017_02
  • Bug fixes
    • Improved handling of HMM logos (some HMMs are unable to be rendered owing to the way they are constructed)

Version 2.9, January 2017

  • Changes
    • UniProt release 2017_01

Version 2.8, December 2016

  • Changes
    • Pfam active sites
    • Ensembl

Version 2.7, September 2016

  • Changes
    • UniProt release 2016_08
    • Gene3D version 14

Version 2.6, August 2016

  • Changes
    • Ensembl Genomes 32
  • Bug fixes
    • Fixes in search and download pages

Version 2.5, July 2016

  • Changes
    • small UI improvements

Version 2.4, June 2016

  • New features
    • Integration of complete Ensembl Plants, and of Ensembl Protists as supported databases for searches.
    • Update to Pfam 30.0
  • Changes
    • More UI changes to the search page

Version 2.3, May 2016

  • New features
    • Integration of Ensembl Bacteria, Ensembl Fungi, Ensembl Metazoa, and Ensembl Plants as supported databases for searches.
  • Changes
    • Small changes in the UI (especially in the search page)
    • Improved performance and better caching

Version 2.2, March 2016

  • New features
    • Integration of Ensembl Genomes as a supported database for searches.
  • Bug fixes
    • Fixed error on selection between iterations of Jackhmmer searches

Version 2.1, January 2016

  • New features
    • RP levels that were previously removed have been reinstated by popular demand.
    • Revisions to the help documentation.
    • PDB search results now link to both PDBe and RCSB.

Version 2.0, August 2015

  • New features
    • Move from Janelia to EBI.
    • Now supporting Ensembl Genomes Plants as a new target database.
    • RP levels removed.

Version 1.4, May 2013

  • New features
    • We have enabled the searching of multiple hmm databases via hmmscan. This allows the results of Gene3D, Superfamily, Pfam and TIGRGAMs to be compared in a single page.
    • The HMM length and the coverage of the HMM is now indicated in the tool tip associated with the domain graphic, located in the ‘sequence features’ section. The HMM length has also been added to the hmmscan results table.
    • The website is now using HMMER version 3.1, with the software due to be released shortly. We have added the option of downloading HMMs in both 3.0 and 3.1 formats.
    • Alignment downloads have been improved, particularly for large alignments, which were often so big that the server would timeout.
    • We have also work on several speed optimisations in the website to improve interactivity.
  • Bug Fixes
    • Based on user feedback, we have updated the validation of E-value cut-offs to allow scientific notation with the exponent as E or e.
    • Fixed issue with long taxon names which are now being truncated to ensure that tree, in taxonomy results visualisation, remains aligned.