{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,3,31]],"date-time":"2023-03-31T15:26:53Z","timestamp":1680276413025},"reference-count":19,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The main two sorts of automatic gene annotation frameworks are <jats:italic>ab initio<\/jats:italic> and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more sensitive methods which are usually applied in aligning inter-species sequences.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here we present a new algorithm called <jats:italic>CAT<\/jats:italic> (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. <jats:italic>CAT<\/jats:italic> is implemented using C scripts and is freely available on the web at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/xat.sourceforge.net\/\" ext-link-type=\"uri\">http:\/\/xat.sourceforge.net\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Examined from different angles, <jats:italic>CAT<\/jats:italic> outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that <jats:italic>CAT<\/jats:italic> combines the specificity and speed of the best intra-species algorithms, like <jats:italic>BLAT<\/jats:italic> and <jats:italic>sim4<\/jats:italic>, with the sensitivity of the best inter-species tools, like <jats:italic>GeneWise<\/jats:italic>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-8-349","type":"journal-article","created":{"date-parts":[[2007,9,19]],"date-time":"2007-09-19T18:13:28Z","timestamp":1190225608000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["A cross-species alignment tool (CAT)"],"prefix":"10.1186","volume":"8","author":[{"given":"Heng","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liang","family":"Guan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tao","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiran","family":"Guo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei-Mou","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gane Ka-Shu","family":"Wong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,9,19]]},"reference":[{"key":"1721_CR1","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1038\/nrg1160","volume":"4","author":"J Wang","year":"2003","unstructured":"Wang J, Li S, Zhang Y, Zheng H, Xu Z, Ye J, Yu J, Wong GK: Vertebrate gene predictions and the problem of large genes. 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