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Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models.

Last news
Jul 2019 Update some tools: hmmer3, mafft and R based tools
Jun 2017 Update of protein databases
Feb 2017 New Dotlet javascript-based available in beta!
Dec 2014 Update mafft to version 7.187
Apr 2014 Update BLASTP/PSI-BLAST to BLAST+ version 2.2.28
Sep 2013 Update mafft to version 7.058b
Sep 2013 Update hmmer3 to version 3.1b1
Aug 2013 Link to new TCoffee server
May 2011 New Web interface
Apr 2010 Add hmmer3 service.
Jun 2009 Add the CS-BLAST tool
Oct 2008 Update of the Jalview applet to release 2.4
Aug 2008 Add a text search to find sequence, motif or taxonomy matches.
Jul 2008 Add mkdom2 and hmmer services.
Jan 2008 A link to RAxML (phylogenetic tree) was added from the MSA hub.
Sep 2007 Profile Align was added to align a set of proteins onto an existent Multiple Sequence Alignment without having to realign the whole sequences.
See Profile Align to use it, or from hubs.
Aug 2007 A new tool to reformat your sequences and your multiple sequence alignments.
See Reformat to use it, or from hubs.
Jun 2007 MyHits: improvements to an interactive resource for analyzing protein sequences.
Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W433-7.   [RIS]
Dec 2006 The Dotlet applet has been updated to version 1.5. See changes for details.
Oct 2006 The pages Query by Motif and Query by Protein allow taxonomic restriction and give a new improved output where the user can send selected hits to the Protein Hub. A long user requested feature.
Sep 2006 The new version (2.1) of the Jalview applet has been modified and incorporated in MyHits. See changes for details.
Jun 2006 A new taxonomic restriction menu was added to the PSI-BLAST, Profile Search and Pattern Search pages where a user can select its own taxonomic id, e.g., 8782 for all birds or 37349 for Woolly Mammoth ;-).
May 2006 Several hardware/software problems impaired our service. We can only apologize for the inconvenience.
Jan 2006 MAFFT a very fast multiple alignment tool has been added.
Sep 2005 The JACOP server is now available to classify your proteins.
WARNING: This service is slow.
Jul 2005 The splice variants of the TrEMBL database is no longer available (see sp_news.html#rel5.5).
As a consequence tr_var will disappear soon from MyHits.
Nov 2004 Two new pages are available: Translator to translate DNA sequences into protein
and Modify User to allow registered user to edit their information.
Oct 2004 A new page describing the current status of the hit lists is available
from the Database menu. Some pages received minor updates.
Aug 2004 HAMAP profiles and TIGRfam HMMs are available on the Motif scan server.
Aug 2004 The Motif Scan and Profile Search servers are available in BETA version.
Please report problems:
Aug 2004 TrEMBL_new section was integrated into TrEMBL.
Jun 2004 Protein section of EnsEMBL was added.
Apr 2004 The server is working again with all databases.
Feb 2004 For technical reasons the server might be partially unusable until February 25. We are sorry for this inconvenience.
Feb 2004 It does not work yet.