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.
|Update some tools: hmmer3, mafft and R based tools
|Update of protein databases
|Update mafft to version 7.187
|Update BLASTP/PSI-BLAST to BLAST+ version 2.2.28
|Update mafft to version 7.058b
|Update hmmer3 to version 3.1b1
|Link to new TCoffee server
|New Web interface
|Add hmmer3 service.
|Add the CS-BLAST tool
|Update of the Jalview applet to release 2.4
|Add a text search to find sequence, motif or taxonomy matches.
|Add mkdom2 and hmmer services.
|A link to RAxML (phylogenetic tree) was added from the MSA hub.
Profile Align was added to align a set of proteins onto an existent
Multiple Sequence Alignment without having to realign the whole
See Profile Align to use it, or from hubs.
A new tool to reformat your sequences and your multiple sequence alignments.
See Reformat to use it, or from hubs.
MyHits: improvements to an interactive resource for analyzing protein sequences.
Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W433-7. [RIS]
|The Dotlet applet has been updated to version 1.5. See changes for details.
|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.
|The new version (2.1) of the Jalview applet has been modified and incorporated in MyHits. See changes for details.
|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 ;-).
|Several hardware/software problems impaired our service. We can only apologize for the inconvenience.
|MAFFT a very fast multiple alignment tool has been added.
The JACOP server is now available to classify your proteins.
WARNING: This service is slow.
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.
Two new pages are available: Translator to translate DNA sequences into protein
and Modify User to allow registered user to edit their information.
A new page describing the current status of the hit lists is available
from the Database menu. Some pages received minor updates.
|HAMAP profiles and TIGRfam HMMs are available on the Motif scan server.
The Motif Scan and Profile Search servers are available in BETA version.
Please report problems:
|TrEMBL_new section was integrated into TrEMBL.
|Protein section of EnsEMBL was added.
|The server is working again with all databases.
|For technical reasons the server might be partially unusable until February 25. We are sorry for this inconvenience.
|It does not work yet.