Using database matches with for HMMGene for automated gene detection in Drosophila

doi:10.1101/gr.10.4.523

Comparative Study

. 2000 Apr;10(4):523-8.

doi: 10.1101/gr.10.4.523.

Using database matches with for HMMGene for automated gene detection in Drosophila

A Krogh¹

Affiliations

PMID: 10779492
PMCID: PMC310864
DOI: 10.1101/gr.10.4.523

Comparative Study

Using database matches with for HMMGene for automated gene detection in Drosophila

A Krogh. Genome Res. 2000 Apr.

. 2000 Apr;10(4):523-8.

doi: 10.1101/gr.10.4.523.

Author

A Krogh¹

Affiliation

¹ Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark. krogh@cbs.dtu.dk

PMID: 10779492
PMCID: PMC310864
DOI: 10.1101/gr.10.4.523

Abstract

The application of the gene finder HMMGene to the Adh region of the Drosophila melanogaster is described, and the prediction results are analyzed. HMMGene is based on a probabilistic model called a hidden Markov model, and the probabilistic framework facilitates the inclusion of database matches of varying degrees of certainty. It is shown that database matches clearly improve the performance of the gene finder. For instance, the sensitivity for coding exons predicted with both ends correct grows from 62% to 70% on a high-quality test set, when matches to proteins, cDNAs, repeats, and transposons are included. The specificity drops more than the sensitivity increases when ESTs are used. This is due to the high noise level in EST matches, and it is discussed in more detail why this is and how it might be improved.

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Comment in

A biologist's view of the Drosophila genome annotation assessment project.
Ashburner M. Ashburner M. Genome Res. 2000 Apr;10(4):391-3. doi: 10.1101/gr.10.4.391. Genome Res. 2000. PMID: 10779478 Review. No abstract available.

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References

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed
1. Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, et al. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: The Adh region. Genetics. 1999;153:179–219. - PMC - PubMed
1. Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 1998;26:38–42. - PMC - PubMed
1. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997;268:78–94. - PubMed
1. Durbin RM, Eddy SR, Krogh A, Mitchison G. Biological sequence analysis. Cambridge, UK: Cambridge University Press; 1998.

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[1] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed

[2] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed

[3] Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, et al. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: The Adh region. Genetics. 1999;153:179–219. - PMC - PubMed

[4] Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, et al. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: The Adh region. Genetics. 1999;153:179–219. - PMC - PubMed

[5] Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 1998;26:38–42. - PMC - PubMed

[6] Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 1998;26:38–42. - PMC - PubMed

[7] Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997;268:78–94. - PubMed

[8] Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997;268:78–94. - PubMed

[9] Durbin RM, Eddy SR, Krogh A, Mitchison G. Biological sequence analysis. Cambridge, UK: Cambridge University Press; 1998.

[10] Durbin RM, Eddy SR, Krogh A, Mitchison G. Biological sequence analysis. Cambridge, UK: Cambridge University Press; 1998.

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Using database matches with for HMMGene for automated gene detection in Drosophila

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Using database matches with for HMMGene for automated gene detection in Drosophila

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