A Strategy to Retrieve the Whole Set of Protein Modules in Microbial Proteomes
Identifieur interne : 000F60 ( Main/Exploration ); précédent : 000F59; suivant : 000F61A Strategy to Retrieve the Whole Set of Protein Modules in Microbial Proteomes
Auteurs : Stéphanie Le Bouder-Langevin ; Isabelle Capron-Montaland ; Renaud De Rosa ; Bernard LabedanSource :
- Genome Research [ 1088-9051 ] ; 2002.
Abstract
Protein homology is often limited to long structural segments that we have previously called modules. We describe here a suite of programs used to catalog the whole set of modules present in microbial proteomes. First, the Darwin AllAll program detects homologous segments using thresholds for evolutionary distance and alignment length, and another program classifies these modules. After assembling these homologous modules in families, we further group families which are related by a chain of neighboring unrelated homologous modules. With the automatic analysis of these groups of families sharing homologous modules in independent multimodular proteins, one can split into their component parts many fused modules and/or deduce by logic more distant modules. All detected and inferred modules are reassembled in refined families. These two last steps are made by a unique program. Eventually, the soundness of the data obtained by this experimental approach is checked using independent tests. To illustrate this modular approach, we compared four proteobacterial proteomes (
Url:
DOI: 10.1101/gr.393902
PubMed: 12466301
PubMed Central: 187581
Affiliations:
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We describe here a suite of programs used to catalog the whole set of modules present in microbial proteomes. First, the Darwin AllAll program detects homologous segments using thresholds for evolutionary distance and alignment length, and another program classifies these modules. After assembling these homologous modules in families, we further group families which are related by a chain of neighboring unrelated homologous modules. With the automatic analysis of these groups of families sharing homologous modules in independent multimodular proteins, one can split into their component parts many fused modules and/or deduce by logic more distant modules. All detected and inferred modules are reassembled in refined families. These two last steps are made by a unique program. Eventually, the soundness of the data obtained by this experimental approach is checked using independent tests. To illustrate this modular approach, we compared four proteobacterial proteomes (<italic>Campylobacter jejuni, Escherichia coli</italic>, <italic>Haemophilus influenzae</italic>, and <italic>Helicobacter pylori</italic>). It appears that this method might retrieve from present-day proteins many of the modules which can help to trace back ancient events of gene duplication and/or fusion.</p></div></front></TEI><affiliations><list></list><tree><noCountry><name sortKey="Capron Montaland, Isabelle" sort="Capron Montaland, Isabelle" uniqKey="Capron Montaland I" first="Isabelle" last="Capron-Montaland">Isabelle Capron-Montaland</name><name sortKey="De Rosa, Renaud" sort="De Rosa, Renaud" uniqKey="De Rosa R" first="Renaud" last="De Rosa">Renaud De Rosa</name><name sortKey="Labedan, Bernard" sort="Labedan, Bernard" uniqKey="Labedan B" first="Bernard" last="Labedan">Bernard Labedan</name><name sortKey="Le Bouder Langevin, Stephanie" sort="Le Bouder Langevin, Stephanie" uniqKey="Le Bouder Langevin S" first="Stéphanie" last="Le Bouder-Langevin">Stéphanie Le Bouder-Langevin</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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