ArticleGenome research2005
Identification of genomic features using microsyntenies of domains: domain teams.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Computational modelling of chromosomally clustering protein domains in bacteria.BMC bioinformatics · 2021Article
- Identification of gene fusion events inNAR genomics and bioinformatics · 2020Article
- Finding approximate gene clusters with Gecko 3.Nucleic acids research · 2016Article
- A unique RPW8-encoding class of genes that originated in early land plants and evolved through domain fission, fusion, and duplication.Scientific reports · 2016Article
- An event-driven approach for studying gene block evolution in bacteria.Bioinformatics (Oxford, England) · 2015Article
- Enzyme reaction annotation using cloud techniques.BioMed research international · 2013Article
- The dynamics and evolutionary potential of domain loss and emergence.Molecular biology and evolution · 2012Article
- Bacterial syntenies: an exact approach with gene quorum.BMC bioinformatics · 2011Article
- A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.PLoS computational biology · 2008Article
- Just how versatile are domains?BMC evolutionary biology · 2008Article
- DIMA 2.0--predicted and known domain interactions.Nucleic acids research · 2008Article
- On the detection of functionally coherent groups of protein domains with an extension to protein annotation.BMC bioinformatics · 2007Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The detection, across several genomes, of local conservation of gene content and proximity considerably helps the prediction of features of interest, such as gene fusions or physical and functional interactions. Here, we want to process realistic models of chromosomes, in which genes (or genomic segments of several genes) can be duplicated within a chromosome, or be absent from some other chromosome(s). Our approach adopts the technique of temporarily forgetting genes and working directly with protein "domains" such as those found in Pfam. This allows the detection of strings of domains that are conserved in their content, but not necessarily in their order, which we refer to as domain teams. The prominent feature of the method is that it relaxes the rigidity of the orthology criterion and avoids many of the pitfalls of gene-families identification methods, often hampered by multidomain proteins or low levels of sequence similarity. This approach, that allows both inter- and intrachromosomal comparisons, proves to be more sensitive than the classical methods based on pairwise sequence comparisons, particularly in the simultaneous treatment of many species. The automated and fast detection of domain teams, together with its increased sensitivity at identifying segments of identical (protein-coding) gene contents as well as gene fusions, should prove a useful complement to other existing methods.
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