Database of Homologous Sequences from Ensembl Complete Genomes

HOMOLENS release 03

January 2007 Previous release

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 Release 41, 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 03 (January 2007).

Species from Ensembl:

Ensembl 41 Organisms Translated CDS

Aedes aegypti 41_1a 11360/0/2/0 (0%/0%/0%)

Anopheles gambiae 41_3d 13510/0/31/0 (0%/0%/0%)

Apis mellifera 38_2d 27755/1/269/0 (0%/0%/0%)

Bos taurus 41_2 32556/7/620/12 (0%/1%/0%)

Caenorhabditis elegans 41_160 25218/1/0/0 (0%/0%/0%)

Canis familiaris 41_1j 29813/0/0/0 (0%/0%/0%)

Caenorhabditis briggsae 25 14712/0/23/1 (0%/0%/0%)

Ciona intestinalis 41_2c 20000/0/128/0 (0%/0%/0%)

Ciona savignyi 41_2b 20150/1/27/0 (0%/0%/0%)

Danio rerio 41_6b 36065/5/361/0 (0%/1%/0%)

Dasypus novemcinctus 40_1 13567/12/8857/0 (0%/65%/0%)

Drosophila melanogaster 41_43 19577/33/1/0 (0%/0%/0%)

Echinops telfairi 40_1 14309/8/9348/0 (0%/65%/0%)

Gallus gallus 41_1p 20667/13/455/0 (0%/2%/0%)

Gasterosteus aculeatus 41_1a 27181/13/138/0 (0%/0%/0%)

Homo sapiens 41_36c 47004/41/6/0 (0%/0%/0%)

Loxodonta africana 40_1 14366/10/9618/0 (0%/66%/0%)

Macaca mulatta 41_10a 36446/14/491/0 (0%/1%/0%)

Monodelphis domestica 41_3a 30358/0/80/0 (0%/0%/0%)

Mus musculus 41_36b 29026/34/2/0 (0%/0%/0%)

Oryctolagus cuniculus 41_1a 13705/4/8615/0 (0%/62%/0%)

Oryzias latipes 41_1 25880/0/546/0 (0%/2%/0%)

Pan troglodytes 41_21 32667/4/739/0 (0%/2%/0%)

Rattus norvegicus 41_34k 32996/34/686/0 (0%/2%/0%)

Saccharomyces cerevisiae 41_1d 4767/2/0/0 (0%/0%/0%)

Takifugu rubripes 41_4c 22102/0/283/0 (0%/1%/0%)

Tetraodon nigroviridis 41_1g 15841/1/225/0 (0%/1%/0%)

Xenopus tropicalis 41_41b 28324/0/626/0 (0%/2%/0%)

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: HOMOLENS contains the protein sequences data while HOMOLENSDNA 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:

The list of the families available in the database.
The sequence (protein or nucleotide) of the genes defining these families.
The alignments built with these families.
The phylogenetic trees computed with these alignments.

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 license@isb-sib.ch).

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.

Acknowledgements

This project is supported

by the European Commission ( TEMBLOR, contract-no. QLRI-CT-2001-00015, RTD programme "Quality of Life and Management of Living Resources") as a part of the Integr8 project and
Calculations have been done at the IN2P3 Computing Center.

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