{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T16:32:01Z","timestamp":1774369921228,"version":"3.50.1"},"reference-count":29,"publisher":"World Scientific Pub Co Pte Ltd","issue":"03","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2006,6]]},"abstract":"<jats:p>In the process of making full-length cDNA, predicting protein coding regions helps both in the preliminary analysis of genes and in any succeeding process. However, unfinished cDNA contains artifacts including many sequencing errors, which hinder the correct evaluation of coding sequences. Especially, predictions of short sequences are difficult because they provide little information for evaluating coding potential. In this paper, we describe ANGLE, a new program for predicting coding sequences in low quality cDNA. To achieve error-tolerant prediction, ANGLE uses a machine-learning approach, which makes better expression of coding sequence maximizing the use of limited information from input sequences. Our method utilizes not only codon usage, but also protein structure information which is difficult to be used for stochastic model-based algorithms, and optimizes limited information from a short segment when deciding coding potential, with the result that predictive accuracy does not depend on the length of an input sequence. The performance of ANGLE is compared with ESTSCAN on four dataset each of them having a different error rate (one frame-shift error or one substitution error per 200\u2013500 nucleotides) and on one dataset which has no error. ANGLE outperforms ESTSCAN by 9.26% in average Matthews's correlation coefficient on short sequence dataset (&lt; 1000 bases). On long sequence dataset, ANGLE achieves comparable performance.<\/jats:p>","DOI":"10.1142\/s0219720006002260","type":"journal-article","created":{"date-parts":[[2006,9,7]],"date-time":"2006-09-07T10:38:49Z","timestamp":1157625529000},"page":"649-664","source":"Crossref","is-referenced-by-count":125,"title":["ANGLE: A SEQUENCING ERRORS RESISTANT PROGRAM FOR PREDICTING PROTEIN CODING REGIONS IN UNFINISHED cDNA"],"prefix":"10.1142","volume":"04","author":[{"given":"KANA","family":"SHIMIZU","sequence":"first","affiliation":[{"name":"Department of Computer Science, Graduate school of Waseda University, 17 301 Kikui-cho, Shinjuku-ku, Tokyo, 162-0044, Japan"}]},{"given":"JUN","family":"ADACHI","sequence":"additional","affiliation":[{"name":"The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu Minato-ku Tokyo, 106-8569, Japan"},{"name":"Department of Biosystems Science, The Graduate University for Advanced Studies, 240-0193 Shonan Village Hayama Kanagawa, Japan"}]},{"given":"YOICHI","family":"MURAOKA","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Graduate School of Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1038\/nature01266"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1126\/science.286.5439.455"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/30.1.166"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1038\/35055500"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkf543"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/17.1.13"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/23.15.2900"},{"key":"rf8","first-page":"117","volume":"11","author":"Xu Y.","journal-title":"Comput. 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