CONTRAST: a Discriminative, Phylogeny-free Approach to Multiple Informant De Novo Gene Prediction

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2007 Dec 22

PMID 18096039

Citations 37

Authors

Samuel S Gross

Chuong B Do

Marina Sirota

Serafim Batzoglou

Affiliations

Soon will be listed here.

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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References

Korf I, Flicek P, Duan D, Brent M . Integrating genomic homology into gene structure prediction. Bioinformatics. 2001; 17 Suppl 1:S140-8. DOI: 10.1093/bioinformatics/17.suppl_1.s140. View

DeCaprio D, Vinson J, Pearson M, Montgomery P, Doherty M, Galagan J . Conrad: gene prediction using conditional random fields. Genome Res. 2007; 17(9):1389-98. PMC: 1950907. DOI: 10.1101/gr.6558107. View

Birney E, Clamp M, Durbin R . GeneWise and Genomewise. Genome Res. 2004; 14(5):988-95. PMC: 479130. DOI: 10.1101/gr.1865504. View

Karolchik D, Baertsch R, Diekhans M, Furey T, Hinrichs A, Lu Y . The UCSC Genome Browser Database. Nucleic Acids Res. 2003; 31(1):51-4. PMC: 165576. DOI: 10.1093/nar/gkg129. View

Keibler E, Brent M . Eval: a software package for analysis of genome annotations. BMC Bioinformatics. 2003; 4:50. PMC: 270064. DOI: 10.1186/1471-2105-4-50. View

Wang M, Buhler J, Brent M . The effects of evolutionary distance on TWINSCAN, an algorithm for pair-wise comparative gene prediction. Cold Spring Harb Symp Quant Biol. 2004; 68:125-30. DOI: 10.1101/sqb.2003.68.125. View

Arumugam M, Wei C, Brown R, Brent M . Pairagon+N-SCAN_EST: a model-based gene annotation pipeline. Genome Biol. 2006; 7 Suppl 1:S5.1-10. PMC: 1810554. DOI: 10.1186/gb-2006-7-s1-s5. View

Baross A, Butterfield Y, Coughlin S, Zeng T, Griffith M, Griffith O . Systematic recovery and analysis of full-ORF human cDNA clones. Genome Res. 2004; 14(10B):2083-92. PMC: 528924. DOI: 10.1101/gr.2473704. View

Bafna V, Huson D . The conserved exon method for gene finding. Proc Int Conf Intell Syst Mol Biol. 2000; 8:3-12. View

10.

Alexandersson M, Cawley S, Pachter L . SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res. 2003; 13(3):496-502. PMC: 430255. DOI: 10.1101/gr.424203. View

11.

Gross S, Brent M . Using multiple alignments to improve gene prediction. J Comput Biol. 2006; 13(2):379-93. DOI: 10.1089/cmb.2006.13.379. View

12.

Parra G, Agarwal P, Abril J, Wiehe T, Fickett J, Guigo R . Comparative gene prediction in human and mouse. Genome Res. 2003; 13(1):108-17. PMC: 430976. DOI: 10.1101/gr.871403. View

13.

Brent M . Genome annotation past, present, and future: how to define an ORF at each locus. Genome Res. 2005; 15(12):1777-86. DOI: 10.1101/gr.3866105. View

14.

Wu J, Garcia A, Hulyk S, Sneed A, Kowis C, Yuan Y . Large-scale RT-PCR recovery of full-length cDNA clones. Biotechniques. 2004; 36(4):690-6, 698-700. DOI: 10.2144/04364DD03. View

15.

Blanchette M, Kent W, Riemer C, Elnitski L, Smit A, Roskin K . Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004; 14(4):708-15. PMC: 383317. DOI: 10.1101/gr.1933104. View

16.

Stanke M, Waack S . Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003; 19 Suppl 2:ii215-25. DOI: 10.1093/bioinformatics/btg1080. View

17.

Pedersen J, Hein J . Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics. 2003; 19(2):219-27. DOI: 10.1093/bioinformatics/19.2.219. View

18.

Wei C, Brent M . Using ESTs to improve the accuracy of de novo gene prediction. BMC Bioinformatics. 2006; 7:327. PMC: 1534067. DOI: 10.1186/1471-2105-7-327. View

19.

Guigo R, Dermitzakis E, Agarwal P, Ponting C, Parra G, Reymond A . Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci U S A. 2003; 100(3):1140-5. PMC: 298740. DOI: 10.1073/pnas.0337561100. View

20.

Carter D, Durbin R . Vertebrate gene finding from multiple-species alignments using a two-level strategy. Genome Biol. 2006; 7 Suppl 1:S6.1-12. PMC: 1810555. DOI: 10.1186/gb-2006-7-s1-s6. View