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Databases of homologous gene families for comparative genomics.

Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perrière G - BMC Bioinformatics (2009)

Bottom Line: HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl.Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface.The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Claude Bernard - Lyon 1, 43 bd, du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. penel@biomserv.univ-lyon1.fr

ABSTRACT

Background: Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the molecular level (speciation, single gene or whole genome duplications, etc.) and phylogenetics. In that context, databases providing users high quality homologous families and sequence alignments as well as phylogenetic trees based on state of the art algorithms are becoming indispensable.

Methods: We developed an automated procedure allowing massive all-against-all similarity searches, gene clustering, multiple alignments computation, and phylogenetic trees construction and reconciliation. The application of this procedure to a very large set of sequences is possible through parallel computing on a large computer cluster.

Results: Three databases were developed using this procedure: HOVERGEN, HOGENOM and HOMOLENS. These databases share the same architecture but differ in their content. HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl. Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface. The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes. The three databases, as well as the software required to build and query them, can be used or downloaded from the PBIL (Pôle Bioinformatique Lyonnais) site at http://pbil.univ-lyon1.fr/.

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Multiple alignments and phylogenetic trees visualization through the PBIL Web interface. In this exemple, the alignment is displayed with the JalView applet and the phylogenetic tree is displayed with the ATV applet.
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Related In: Results  -  Collection

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Figure 3: Multiple alignments and phylogenetic trees visualization through the PBIL Web interface. In this exemple, the alignment is displayed with the JalView applet and the phylogenetic tree is displayed with the ATV applet.

Mentions: Alignments can be displayed on static HTML pages with several colouring options and they can be edited in order to visualize only a subset of sequences (Figure 3). Alternatively they can be visualised with the JalView applet [40] or downloaded on local disk. Phylogenetic trees are displayed as a clickable Portable Network Graphics (PNG) picture generated with Perl modules [41] and coloured according to taxonomy. Several displaying options are available, allowing to visualize species names, sequence name. Alternatively, trees can be visualised with the ATV applet [42] or downloaded.


Databases of homologous gene families for comparative genomics.

Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perrière G - BMC Bioinformatics (2009)

Multiple alignments and phylogenetic trees visualization through the PBIL Web interface. In this exemple, the alignment is displayed with the JalView applet and the phylogenetic tree is displayed with the ATV applet.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697650&req=5

Figure 3: Multiple alignments and phylogenetic trees visualization through the PBIL Web interface. In this exemple, the alignment is displayed with the JalView applet and the phylogenetic tree is displayed with the ATV applet.
Mentions: Alignments can be displayed on static HTML pages with several colouring options and they can be edited in order to visualize only a subset of sequences (Figure 3). Alternatively they can be visualised with the JalView applet [40] or downloaded on local disk. Phylogenetic trees are displayed as a clickable Portable Network Graphics (PNG) picture generated with Perl modules [41] and coloured according to taxonomy. Several displaying options are available, allowing to visualize species names, sequence name. Alternatively, trees can be visualised with the ATV applet [42] or downloaded.

Bottom Line: HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl.Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface.The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Claude Bernard - Lyon 1, 43 bd, du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. penel@biomserv.univ-lyon1.fr

ABSTRACT

Background: Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the molecular level (speciation, single gene or whole genome duplications, etc.) and phylogenetics. In that context, databases providing users high quality homologous families and sequence alignments as well as phylogenetic trees based on state of the art algorithms are becoming indispensable.

Methods: We developed an automated procedure allowing massive all-against-all similarity searches, gene clustering, multiple alignments computation, and phylogenetic trees construction and reconciliation. The application of this procedure to a very large set of sequences is possible through parallel computing on a large computer cluster.

Results: Three databases were developed using this procedure: HOVERGEN, HOGENOM and HOMOLENS. These databases share the same architecture but differ in their content. HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl. Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface. The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes. The three databases, as well as the software required to build and query them, can be used or downloaded from the PBIL (Pôle Bioinformatique Lyonnais) site at http://pbil.univ-lyon1.fr/.

Show MeSH