ArticleBMC bioinformatics2007
Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies.Scientific reports · 2018Article
- Regulators of plant biomass degradation in ascomycetous fungi.Biotechnology for biofuels · 2017Review
- Closely related fungi employ diverse enzymatic strategies to degrade plant biomass.Biotechnology for biofuels · 2015Article
- Prevalence of transcription factors in ascomycete and basidiomycete fungi.BMC genomics · 2014Article
- Cytotoxic and pathogenic properties of Klebsiella oxytoca isolated from laboratory animals.PloS one · 2014Article
- Identification of MFS proteins in sorghum using semantic similarity.Theory in biosciences = Theorie in den Biowissenschaften · 2013Article
- Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods.PloS one · 2013Article
- LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria.BMC genomics · 2010Article
- ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.Bioinformatics (Oxford, England) · 2010Article
- Enrichment of homologs in insignificant BLAST hits by co-complex network alignment.BMC bioinformatics · 2010Article
- MetaMine--a tool to detect and analyse gene patterns in their environmental context.BMC bioinformatics · 2008Article
- Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes.Genome biology · 2008Article
- Using genome-wide protein sequence data to predict amino acid conservation.The protein journal · 2008Article
- SynBlast: assisting the analysis of conserved synteny information.BMC bioinformatics · 2008Article
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2 authors.
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Abstract
backgroundHomology is a key concept in both evolutionary biology and genomics. Detection of homology is crucial in fields like the functional annotation of protein sequences and the identification of taxon specific genes. Basic homology searches are still frequently performed by pairwise search methods such as BLAST. Vast improvements have been made in the identification of homologous proteins by using more advanced methods that use sequence profiles. However additional improvement could be made by exploiting sources of genomic information other than the primary sequence or tertiary structure.
resultsWe test the hypothesis that extrinsic gene properties gene length and gene order can be of help in differentiating spurious sequence similarity from homology in the gray zone. Sharing gene order and similarity in size dramatically increase the chance of a query-hit pair being homologous: gray zone query-hit pairs of similar size and with conserved gene order are homologous in 99% of all cases, while for query-hit pairs without gene order conservation and with different sizes this is only 55%.
conclusionWe have shown that using gene length and gene order drastically improves the detection of homologs within the BLAST gray zone. Our findings suggest that the use of such extrinsic gene properties can also improve the performance of homology detection by more advanced methods, and our study thereby underscores the importance of true data integration for fully exploiting genomic information.
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