Gene recognition by combination of several gene-finding programs |
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| Authors: | Murakami, K Takagi, T |
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| Affiliation: | 1Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku, Tokyo 108-8639 and 2Central Research Laboratory, Hitachi Ltd, 1-280 Higashi-Koigakubo, Kokubunji- shi, Tokyo 185-8601, Japan. |
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| Abstract: | MOTIVATION: A number of programs have been developed to predict theeukaryotic gene structures in DNA sequences. However, gene finding is stilla challenging problem. RESULTS: We have explored the effectiveness when theresults of several gene-finding programs were re- analyzed and combined. Westudied several methods with four programs (FEXH, GeneParser3, GEN-SCAN andGRAIL2). By HIGHEST-policy combination method or BOUNDARY method,approximate correlation (AC) improved by 3- 5% in comparison with the bestsingle gene-finding program. From another viewpoint, OR-based combinationof the four programs is the most reliable to know whether a candidate exonoverlaps with the real exon or not, although it is less sensitive thanGENSCAN for exon-intron boundaries. Our methods can easily be extended tocombine 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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