ArticleBMC bioinformatics2011
Identification of conserved gene clusters in multiple genomes based on synteny and homology.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 11 citations in OpenAlex.
- In vivo and in silico screening for antimicrobial compounds from cyanobacteria.MicrobiologyOpen · 2022Review
- Article
- GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm.BMC evolutionary biology · 2016Article
- Quantitative synteny scoring improves homology inference and partitioning of gene families.BMC bioinformatics · 2013Article
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundUncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on gene teams and homology teams.
resultsOur primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete phylum.
conclusionsThe result is an efficient algorithm that works on multiple genomes, considers paralogous copies of genes and is able to uncover orthologous clusters even in distant genomes. Resulting orthologous clusters are comparable to those obtained by manual curation.
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