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eggNOG

http://eggnog.embl.de/

Description :
Evolutionary genealogy of genes: Non-supervised Orthologous Groups

EPGD

http://epgd.biosino.org/EPGD/

Description :
Eukaryotic Paralog Group Database

OPTIC

http://genserv.anat.ox.ac.uk/

Description :
Orthologous and Paralogous Transcripts in Clades

OrthoDB

http://cegg.unige.ch/orthodb/browse

Description :
An hierarchical catalog of orthologous proteins in metazoa

PhyloFacts

http://phylogenomics.berkeley.edu/phylofacts/

Description :
The PhyloFacts resource contains pre-calculated structural and phylogenomic analysis of over 15,000 protein family "books" across the Tree of Life. Each book includes a multiple sequence alignment, one or more phylogenetic trees, predicted subfamilies, predicted 3D protein structures, active sites and other key residues, cellular localization, and Gene Ontology (GO) annotations and evidence codes. PhyloFacts includes hidden Markov models for classification of user-submitted (DNA or protein) sequences to protein families and subfamilies. Our current focus is on covering all the gene families represented in the human genome and all structural domains, but plan to expand the resource to include all proteins in all species. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary framework.

Aknowledgement :
This work was supported by a Presidential Early Career Award for Scientists and Engineers (PECASE) from the National Science Foundation, and by an RO1 from the National Human Genome Research Institute of the NIH.

References :
1. Krishnamurthy, N., Brown, D., Kirshner, D. and Sjölander, K. (2006). PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification. Genome Biology, 7(9):R83.

Selectome

http://bioinfo.unil.ch/selectome/

Description :
Gene trees that show positive selection

HOINVGEN

http://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html

Description :
INVHOGEN (INVertebrate HOmologous GENes) is a database combining the available invertebrate protein genes from UniProt (consisting of Swiss-Prot, TrEMBL) into gene families. For each family INVHOGEN provides a multiple protein alignment, a maximum likelihood based phylogenetic tree, and taxonomic information about the sequences. It is possible to download the corresponding GenBank flatfiles, the alignment and the tree in Newick format. Sequences and related information have been structured in an ACNUC database under a client/server architecture. Thus, complex selections can be performed. An external graphical tool allows access to the data to evaluate homology relationships between genes and distinguish orthologous from paralogous sequences. INVHOGEN complements the well-known HOVERGEN database.

Aknowledgement :
This work was supported by a grant from the Deutsche Forschungsgemeinschaft (DFG: SFB-TR1). Funding to pay the Open Access publication charges for this article was provided by the Deutsche Forschungsgemeinschaft.

References :
1. Gouy,M., Gautier,C., Attimonelli,M., Lanave,C., di Paola,G. (1985) ACNUCÐa portable retrieval system for nucleic acid sequence databases: Logical and physical designs and usage. Comput. Applic. Biosci., 1, 167-172.
2. Duret,L., Perriere,G. and Gouy,M. (1999) HOVERGEN: database and software for comparative analysis of homologous vertebrate genes. In Bioinformatics and Systems, Letovsky, S. (ed.), Kluwer Academic Publishers, Boston, pp. 13-29.

Roundup

Description :
Orthologs and corresponding evolutionary distances

Strepto_DB

http://oger.tu-bs.de/strepto_db

Description :
Database for comparative genome analysis of 15 strains of the genus Streptococcus

PhyloPat

http://www.cmbi.ru.nl/phylopat

Description :
Phylogenetic patterns of genes from the Ensembl database

SPEED

http://bioinfobase.umkc.edu/speed/speed_main.htm

Description :
Searchable prototype experimental evolutionary database

Evola

http://jbirc.jbic.or.jp/hinv/evola/

Description :
Human genes and their vertebrate orthologs

OGtree

http://bioalgorithm.life.nctu.edu.tw/OGtree/

Description :
Overlapping genes (OG) in prokaryotic species are used in OGtree to construct genome phylogeny trees. Overlapping gene content and overlapping gene order of the whole genome is used for the distance based method of tree construction.

Signature

http://www.cmbi.ru.nl/signature

Description :
Signature identifies signature genes or genes that are unique to a taxonomic clade and thus useful in phylogenetic analysis. Users input a set of query sequences and returned is a list of taxonomic clades that share signatures with the query.

GeConT 2

http://gecont.ibt.unam.mx/cgi-bin/gecont/gecont.pl

Description :
The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.

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