Finding Genes in DNA with a Hidden Markov Model
| dc.contributor.author | Henderson, John | |
| dc.contributor.author | Salzberg, Steven | |
| dc.contributor.author | Fasman, Kenneth H | |
| dc.date.accessioned | 2008-06-18T13:26:43Z | |
| dc.date.available | 2008-06-18T13:26:43Z | |
| dc.date.issued | 1997 | |
| dc.description.abstract | This study describes a new Hidden Markov Model (HMM) system for segmenting uncharacterized genomic DNA sequences into exons, introns, and intergenic regions. Separate HMM modules were designed and trained for specific regions of DNA: exons, introns, intergenic regions, and splice sites. The models were then tied together to form a biologically feasible topology. The integrated HMM was trained further on a set of eukaryotic DNA sequences, and tested by using it to segment a separate set of sequences. The resulting HMM system, which is called VEIL (Viterbi Exon-Intron Locator), obtains an overall accuracy on test data of 92% of total bases correctly labelled, with a correlation coefficient of 0.73. Using the more stringent test of exact exon prediction, VEIL correctly located both ends of 53% of the coding exons, and 49% of the exons it predicts are exactly correct. These results compare favorably to the best previous results for gene structure prediction, and demonstrate the benefits of using HMMs for this problem. | en |
| dc.format.extent | 249205 bytes | |
| dc.format.mimetype | application/pdf | |
| dc.identifier.citation | Finding Genes in Human DNA with a Hidden Markov Model. J. Henderson, S.L. Salzberg, and K. Fasman. This describes the VEIL system for finding genes. Journal of Computational Biology 4:2 (1997), 127-141. | en |
| dc.identifier.uri | http://hdl.handle.net/1903/8004 | |
| dc.language.iso | en_US | en |
| dc.publisher | Journal of Computational Biology | en |
| dc.relation.isAvailableAt | College of Computer, Mathematical & Physical Sciences | en_us |
| dc.relation.isAvailableAt | Computer Science | en_us |
| dc.relation.isAvailableAt | Digital Repository at the University of Maryland | en_us |
| dc.relation.isAvailableAt | University of Maryland (College Park, MD) | en_us |
| dc.subject | Hidden Markov Model (HMMM) | en |
| dc.subject | exons | en |
| dc.subject | introns | en |
| dc.subject | intergenic regions | en |
| dc.subject | DNA | en |
| dc.subject | VEIL (Viterbi Exon/Intron Locator) | en |
| dc.title | Finding Genes in DNA with a Hidden Markov Model | en |
| dc.type | Article | en |