ArticleBioinformatics (Oxford, England)2007
Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure.
Article in Bioinformatics (Oxford, England), 2007. 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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4 citing papers in PubMed, 15 citations in OpenAlex.
- ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection.BioMed research international · 2013Article
- Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.American journal of human genetics · 2011Article
- nGASP--the nematode genome annotation assessment project.BMC bioinformatics · 2008Article
- Spliceosomal introns as tools for genomic and evolutionary analysis.Nucleic acids research · 2008Review
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2 authors at 1 institution in 1 country.
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Abstract
motivationCorrect gene predictions are crucial for most analyses of genomes. However, in the absence of transcript data, gene prediction is still challenging. One way to improve gene-finding accuracy in such genomes is to combine the exons predicted by several gene-finders, so that gene-finders that make uncorrelated errors can correct each other.
resultsWe present a method for combining gene-finders called Genomix. Genomix selects the predicted exons that are best conserved within and/or between species in terms of sequence and intron-exon structure, and combines them into a gene structure. Genomix was used to combine predictions from four gene-finders for Caenorhabditis elegans, by selecting the predicted exons that are best conserved with C.briggsae and C.remanei. On a set of approximately 1500 confirmed C.elegans genes, Genomix increased the exon-level specificity by 10.1% and sensitivity by 2.7% compared to the best input gene-finder. AVAILABILITY: Scripts and Supplementary Material can be found at http://www.sanger.ac.uk/Software/analysis/genomix
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.