Mining genes in DNA using genescout

Document Type

Conference Proceeding

Publication Date

12-1-2002

Abstract

In this paper, we present a new system, called GeneScout, for predicting gene structures in vertebrate genomic DNA. The system contains specially designed hidden Markov models (HMMs) for detecting functional sites including protein-translation start sites, mRNA splicing junction donor and acceptor sites, etc. Our main hypothesis is that, given a vertebrate genomic DNA sequence S, it is always possible to construct a directed acyclic graph G such that the path for the actual coding region of S is in the set of all paths on G. Thus, the gene detection problem is reduced to that of analyzing the paths in the graph G. A dynamic programming algorithm is used to find the optimal path in G. The proposed system is trained using an expectation-maximization (EM) algorithm and its performance on vertebrate gene prediction is evaluated using the 10-way cross-validation method. Experimental results show the good performance of the proposed system and its complementarity to a widely used gene detection system. © 2002 IEEE.

Identifier

78149338925 (Scopus)

ISBN

[0769517544, 9780769517544]

Publication Title

Proceedings IEEE International Conference on Data Mining Icdm

ISSN

15504786

First Page

733

Last Page

736

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