ArticleGenome biology2007
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Comparative Genome Annotation.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Building the Chordata Olfactory Receptor Database using more than 400,000 receptors annotated by Genome2OR.Science China. Life sciences · 2022Article
- Translation and natural selection of micropeptides from long non-canonical RNAs.Nature communications · 2022Article
- Ancient evolutionary signals of protein-coding sequences allow the discovery of new genes in the Drosophila melanogaster genome.BMC genomics · 2020Article
- A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers.GigaScience · 2020Article
- Whole-Genome Alignment and Comparative Annotation.Annual review of animal biosciences · 2019Review
- OMGene: mutual improvement of gene models through optimisation of evolutionary conservation.BMC genomics · 2018Article
- A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes.Genome biology · 2016Article
- Simultaneous gene finding in multiple genomes.Bioinformatics (Oxford, England) · 2016Article
- Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.Nucleic acids research · 2016Article
- Stepwise approach for combining many sources of evidence for site-recognition in genomic sequences.BMC bioinformatics · 2016Article
- A Study of Domain Adaptation Classifiers Derived From Logistic Regression for the Task of Splice Site Prediction.IEEE transactions on nanobioscience · 2016Article
- Computational Identification of Novel Genes: Current and Future Perspectives.Bioinformatics and biology insights · 2016Review
- The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum.BMC genomics · 2015Article
- ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection.BioMed research international · 2013Article
- Mutations in C4orf26, encoding a peptide with in vitro hydroxyapatite crystal nucleation and growth activity, cause amelogenesis imperfecta.American journal of human genetics · 2012Article
- A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA).Journal of computational biology : a journal of computational molecular cell biology · 2012Review
- A beginner's guide to eukaryotic genome annotation.Nature reviews. Genetics · 2012Review
- Article
- CTF: a CRF-based transcription factor binding sites finding system.BMC genomics · 2012Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We describe CONTRAST, a gene predictor which directly incorporates information from multiple alignments rather than employing phylogenetic models. This is accomplished through the use of discriminative machine learning techniques, including a novel training algorithm. We use a two-stage approach, in which a set of binary classifiers designed to recognize coding region boundaries is combined with a global model of gene structure. CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art method, misses 46% fewer exons and displays comparable gains in specificity.
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Registered trials
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.