{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:00Z","timestamp":1674710400403},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Repeats detection problems are traditionally formulated as string matching or signal processing problems. They cannot readily handle gaps between repeat units and are incapable of detecting repeat patterns shared by multiple sequences. This study detects short adjacent repeats with interunit insertions from multiple sequences. For biological sequences, such studies can shed light on molecular structure, biological function and evolution.<\/jats:p>\n               <jats:p>Results: The task of detecting short adjacent repeats is formulated as a statistical inference problem by using a probabilistic generative model. An Markov chain Monte Carlo algorithm is proposed to infer the parameters in a de novo fashion. Its applications on synthetic and real biological data show that the new method not only has a competitive edge over existing methods, but also can provide a way to study the structure and the evolution of repeat-containing genes.<\/jats:p>\n               <jats:p>Availability: The related C++ source code and datasets are available at http:\/\/ihome.cuhk.edu.hk\/%7Eb118998\/share\/BASARD.zip.<\/jats:p>\n               <jats:p>Contact: \u00a0xfan@sta.cuhk.edu.hk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr287","type":"journal-article","created":{"date-parts":[[2011,5,7]],"date-time":"2011-05-07T00:34:56Z","timestamp":1304728496000},"page":"1772-1779","source":"Crossref","is-referenced-by-count":3,"title":["An MCMC algorithm for detecting short adjacent repeats shared by multiple sequences"],"prefix":"10.1093","volume":"27","author":[{"given":"Qiwei","family":"Li","sequence":"first","affiliation":[{"name":"1 Department of Statistics and 2Department of Information Engineering, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong"}]},{"given":"Xiaodan","family":"Fan","sequence":"additional","affiliation":[{"name":"1 Department of Statistics and 2Department of Information Engineering, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong"}]},{"given":"Tong","family":"Liang","sequence":"additional","affiliation":[{"name":"1 Department of Statistics and 2Department of Information Engineering, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong"}]},{"given":"Shuo\u2212Yen R.","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Statistics and 2Department of Information Engineering, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong"}]}],"member":"286","published-online":{"date-parts":[[2011,5,6]]},"reference":[{"key":"2023012512014748700_B1","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023012512014748700_B2","doi-asserted-by":"crossref","first-page":"D102","DOI":"10.1093\/nar\/gkm955","article-title":"JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update","volume":"36","author":"Bryne","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012512014748700_B3","doi-asserted-by":"crossref","first-page":"2280","DOI":"10.1109\/TSP.2003.815396","article-title":"Detection and visualization of tandem repeats in DNA sequences","volume":"51","author":"Buchner","year":"2003","journal-title":"IEEE Trans. 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