First release of HOGENOM, a database of homologous genes from complete genome

Equipe Bioinformatique et Génomique EvolutiveLaboratoire de Biométrie et Biologie Evolutive

Université Claude Bernard - Lyon 1

Simon Penel, Laurent Duret, Pascal Calvat, Jean-François Dufayard, Guy Perrière, Manolo Gouy.

POSTER JO 60

Homologous Genes Databases

Research fields:• Proteome/genome comparative analysis

• Phylogenetic studies

• Orthology/Paralogy relationship assignments

• Development of generic databases, specialised databases

– HOVERGEN: families of homologous vertebrate genes

– HOBACGEN: families of homologous bacterial genes

– NureBase, RTKdb, Hoppsigen, Mitalib, Polymorphix..

Contents:

• Nucleic and protein sequences

• Sequence annotations

• Taxonomic data

• Protein multiple alignments

• Phylogenetic trees

The HoGenom database:Homologous Genes Families from

fully Sequenced OrganismsEuropean project TEMBLOR

The HoGenom database:Building of Database

European Bioinformatic Institute

Data selection

1 sequence many species

Proteome sets

Rat

etc.

MouseHuman

SwissProt TrEMBL TrEMBL-new

Protein sequences

1 sequence 1 species

Filtering (SEG)

Local pairwise alignments

The HoGenom database:Building of Database

Similarity search

BLASTP

BLOSUM62E ≤ 10-4

Parralelised calculations at IN2P3

Clustering into familiesA

B

A

C

HSP ≥ 80 % lengthSimilarity ≥ 50 %

1 : Clustering of complete sequences into families2 : Including partial sequences to the families defined previously

The HoGenom database:Building of Database

C

B

A

Cluster A, B, C

Protein Family

Protein family

ABCDEFG

BIONJ

Neighbor joining,Observed divergence

Partial sequences: distance matrix with missing values

Multiple alignment

ABCDEFG

Rooting: mid-point

Phylogenetic treeG

F

E

D

C

B

A

CLUSTAL W

Default parameters

Alignments and trees

The HoGenom database:Building of Database

1016

91

Arabidopsis thaliana (plant) Caenorhabditis elegans (nematod) Drosophila melanogaster (fly) Encephalitozoon cuniculi (microsporidia) Guillardia theta (alguae) Homo sapiens (man) Mus musculus (mouse) Rattus norvegicus (rat) Saccharomyces cerevisiae (yeast) Schizosaccharomyces pombe (fungus)

423 577 proteins,527 925 cds

41 907 families

31%

9%

60%

117 organisms

The HoGenom database:Contents

WWW QueryQuery on sequences and families according to multiple

criteria

Cross Taxa Query on families according to complex taxonomic

criteria

Querying the databases

POSTER JO-60à suivre…