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PubMed · 9789092

Gene recognition by combination of several gene-finding programs.

K Murakami·T Takagi
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Abstract

MOTIVATION: A number of programs have been developed to predict the eukaryotic gene structures in DNA sequences. However, gene finding is still a challenging problem. RESULTS: We have explored the effectiveness when the results of several gene-finding programs were re-analyzed and combined. We studied several methods with four programs (FEXH, GeneParser3, GEN-SCAN and GRAIL2). By HIGHEST-policy combination method or BOUNDARY method, approximate correlation (AC) improved by 3-5% in comparison with the best single gene-finding program. From another viewpoint, OR-based combination of the four programs is the most reliable to know whether a candidate exon overlaps with the real exon or not, although it is less sensitive than GENSCAN for exon-intron boundaries. Our methods can easily be extended to combine other programs. AVAILABILITY: We have developed a server program (Shirokane System) and a client program (GeneScope) to use the methods. GeneScope is available through a WWW site (http://gf.genome.ad.jp/). CONTACT: (katsu,takagi)@ims.u-tokyo.ac.jp

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K Murakami, T Takagi. 1998. Gene recognition by combination of several gene-finding programs.. https://doi.org/10.1093/bioinformatics%2F14.8.665

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