Database of Homologous Sequences from Ensembl Complete Genomes

HOMOLENS release 01

May 2005
Release informations: Protein Nucleotide

Query HOMOLENS

Search Keyword Protein sequences Nucleotide sequences
Search Sequence Protein sequences Nucleotide sequences

HOMOLENS

HOMOLENS is a database of homologous genes from Ensembl fully sequenced organisms, structured under ACNUC sequence database management system. It allows one to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. Thus HOMOLENS is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generaly, HOMOLENS gives an overall view of what is known about a peculiar gene family.

Content

The genome part of HOMOLENS is directly generated from Ensembl. The protein part contains the protein coded by the CDS from Ensembl, and the associated protein annotations. Thus HOMOLENS associates the Ensembl information and the phylogeny of the genes, which is of great interest for phylogenetics and comparative genomics.

There are some cases where one Ensembl gene is associated to more than one CDS (because one gene may give more than one protein, e.g. via alternative splicing). In that case, we select the longest CDS as the representative of that gene. This is the protein encoded by this CDS that is included in the multiple alignment and in the phylogenetic tree.

The sequences are clustered into families with the same method used for HOVERGEN, described here.

Species Ensembl Release
Apis mellifera ( bee) Ensembl bee Genome rel 24 - Arnel1.1 (Oct 2004)
Caenorhabditis briggsae Ensembl cbriggsae Genome rel 24 - cb25.agp8 (Oct 2004)
Caenorhabditis elegans (nematode) Ensembl celegans Genome rel 24 - WS 116 (Oct 2004)
Gallus gallus (chicken) Ensembl chicken Genome rel 24 - WASHUC1 (Oct 2004)
Drosophila melanogaster (fly) Ensembl fruitfly Genome rel 24 - DBGP3.1 (Oct 2004)
Fugu rubripes Ensembl fugu Genome rel 24 - Fugu v2.0 (Oct 2004)
Homo sapiens (human) Ensembl human Genome rel 24 - NCBI34 (Oct 2004)
Anopheles gambiae (mosquito) Ensembl mosquito Genome rel 24 - MOZ 2 (Oct 2004)
Mus musculus (mouse) Ensembl mouse Genome rel 24 - NCBI m33 (Oct 2004)
Rattus norvegicus (rat) Ensembl rat Genome rel 24 - RGSC 3.1 (Oct 2004)
Tetraodon nigroviridis Ensembl tetraodon Genome rel 24 - TETRAODON7 (Oct 2004)
Danio rerio (zebrafish) Ensembl zebrafish Genome rel 24 - WTSI Zv4 (Oct 2004)
Pan troglodytes Ensembl chimp Genome rel 24 - CHIMP1 (Oct 2004)
Canis familiaris (dog) Ensembl dog Genome rel 27 - BROADD1 (Dec 2004)

WWW access

It is possible to query the database on this server through the WWW-Query and Cross-Taxa systems. Note that HOMOLENS is splitted into two databases on this server: HOMOLENSPROT contains the protein sequences data while HOMOLENSUCL contains the nucleotide sequences.

FamFetch Graphical User Interface

FamFetch is a graphical interface, specifically developped to query databases of gene families. FamFetch is based on a client/server architecture. To access the database you only need to install the FamFetch application on your computer. This program, written in Java, integrates a GUI that allows users to easily access and visualize: In FamFetch phylogenetic trees, genes are colored according to the species from which they come. The user can modify the color table according to the taxa (any taxonomic level) he is interested in. This color table is saved in a file of preferences (named .famfetch in UNIX, FamFetch.Prefs in MaOS, HobacFetch.ini in Windows systems). The color table that is installed by default with FamFetch is dedicated to prokaryotes (for the HOBACGEN database). You can replace this preference file by the one we have prepared for HOGENOM, that is available here.

Important note: the SWISS-PROT entries such as those found in HOGENOM are copyrighted. They are produced through a collaboration between the Swiss Institute of Bioinformatics and the European Bioinformatics Institute. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Usage by and for commercial entities requires a license agreement (See or send an Email to license@isb-sib.ch).

Contact and reference

If you encounter some problems when installing or using HOGENOM, please contact Laurent Duret. Also we welcome any comments or suggestions on the database and/or its interface.

Acknowledgements

This project is supported
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