Database of Homologous Sequences from Ensembl Complete Genomes

HOMOLENS release 02

January 2006 Previous release
Release informations: Protein Nucleotide


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


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.


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.

The present version of HOMOLENS is release 02 (January 2006). It contains a total of 357,409 sequences protein sequences (and 533,802 cds) classified in 97,917 families.

Among all the proteins included in this release 286,102 (80%) are classified into 26,310 families containing at least two sequences and 71,307 (20%) are unique in their family.

Species from Ensembl:

Apis mellifera - Release 34
Anopheles gambiae - Release 34
Bos taurus - Release 36
Canis familiaris - Release 34
Caenorhabditis briggsae - Release 34
Caenorhabditis elegans - Release 34
Ciona intestinalis - Release 34
Danio rerio - Release 34
Drosophila melanogaster - Release 34
Fugu rubripes - Release 36
Gallus gallus - Release 34
Homo sapiens - Release 34
Macaca mulatta - Release 34
Monodelphis domestica - Release 36
Mus musculus - Release 34
Pan troglodytes - Release 34
Rattus norvegicus - Release 34
Saccharomyces cerevisiae - Release 34
Tetraodon nigroviridis - Release 34
Xenopus tropicalis - Release 34

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: SWISS-PROT entries such as those found in HOMOLENS 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

Contact and reference

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


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