Gene Finding in Novel Genomes

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2004 May 18

PMID 15144565

Citations 1616

Authors

Ian Korf

Affiliations

Soon will be listed here.

Abstract

Background: Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.

Results: I introduce the SNAP gene finder which has been designed to be easily adaptable to a variety of genomes. In novel genomes without an appropriate gene finder, I demonstrate that employing a foreign gene finder can produce highly inaccurate results, and that the most compatible parameters may not come from the nearest phylogenetic neighbor. I find that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate.

Conclusion: Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.

Citing Articles

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References

Kulp D, Haussler D, Reese M, Eeckman F . A generalized hidden Markov model for the recognition of human genes in DNA. Proc Int Conf Intell Syst Mol Biol. 1996; 4:134-42. View

Stajich J, Block D, Boulez K, Brenner S, Chervitz S, Dagdigian C . The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002; 12(10):1611-8. PMC: 187536. DOI: 10.1101/gr.361602. View

KROGH A . Two methods for improving performance of an HMM and their application for gene finding. Proc Int Conf Intell Syst Mol Biol. 1997; 5:179-86. View

Solovyev V, Salamov A . The Gene-Finder computer tools for analysis of human and model organisms genome sequences. Proc Int Conf Intell Syst Mol Biol. 1997; 5:294-302. View

Boeddrich A, Burgtorf C, Francis F, Hennig S, Panopoulou G, Steffens C . Sequence analysis of an amphioxus cosmid containing a gene homologous to members of the aldo-keto reductase gene superfamily. Gene. 1999; 230(2):207-14. DOI: 10.1016/s0378-1119(99)00079-7. View

Burge C, Karlin S . Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997; 268(1):78-94. DOI: 10.1006/jmbi.1997.0951. View

Reese M, Hartzell G, Harris N, Ohler U, Abril J, Lewis S . Genome annotation assessment in Drosophila melanogaster. Genome Res. 2000; 10(4):483-501. PMC: 310877. DOI: 10.1101/gr.10.4.483. View

Parra G, Blanco E, Guigo R . GeneID in Drosophila. Genome Res. 2000; 10(4):511-5. PMC: 310871. DOI: 10.1101/gr.10.4.511. View

Bedell J, Korf I, Gish W . MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics. 2001; 16(11):1040-1. DOI: 10.1093/bioinformatics/16.11.1040. View

10.

Lim L, Burge C . A computational analysis of sequence features involved in recognition of short introns. Proc Natl Acad Sci U S A. 2001; 98(20):11193-8. PMC: 58706. DOI: 10.1073/pnas.201407298. View

11.

Kraemer E, Wang J, Guo J, Hopkins S, Arnold J . An analysis of gene-finding programs for Neurospora crassa. Bioinformatics. 2001; 17(10):901-12. DOI: 10.1093/bioinformatics/17.10.901. View

12.

Akashi H . Gene expression and molecular evolution. Curr Opin Genet Dev. 2001; 11(6):660-6. DOI: 10.1016/s0959-437x(00)00250-1. View

13.

Cawley S, Wirth A, Speed T . Phat--a gene finding program for Plasmodium falciparum. Mol Biochem Parasitol. 2001; 118(2):167-74. DOI: 10.1016/s0166-6851(01)00363-2. View

14.

Sakata K, Nagamura Y, Numa H, Antonio B, Nagasaki H, Idonuma A . RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Res. 2001; 30(1):98-102. PMC: 99141. DOI: 10.1093/nar/30.1.98. View

15.

Webb C, Shabalina S, Ogurtsov A, Kondrashov A . Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae. Nucleic Acids Res. 2002; 30(5):1233-9. PMC: 101251. DOI: 10.1093/nar/30.5.1233. View

16.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

17.

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

18.

Majoros W, Pertea M, Antonescu C, Salzberg S . GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Res. 2003; 31(13):3601-4. PMC: 168934. DOI: 10.1093/nar/gkg527. View

19.

Riboldi Tunnicliffe G, Gloeckner G, Elgar G, Brenner S, Rosenthal A . Comparative analysis of the PCOLCE region in Fugu rubripes using a new automated annotation tool. Mamm Genome. 2000; 11(3):213-9. DOI: 10.1007/s003350010039. View