{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:23:07Z","timestamp":1773271387150,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: A quantitative study of molecular evolutionary events such as substitutions, insertions and deletions from closely related genomes requires (1) an accurate multiple sequence alignment program and (2) a method to annotate the insertions and deletions that explain the \u2018gaps\u2019 in the alignment. Although the former requirement has been extensively addressed, the latter problem has received little attention, especially in a comprehensive probabilistic framework.<\/jats:p><jats:p>Results: Here, we present Indelign, a program that uses a probabilistic evolutionary model to compute the most likely scenario of insertions and deletions consistent with an input multiple alignment. It is also capable of modifying the given alignment so as to obtain a better agreement with the evolutionary model. We find close to optimal performance and substantial improvement over alternative methods, in tests of Indelign on synthetic data. We use Indelign to analyze regulatory sequences in Drosophila, and find an excess of insertions over deletions, which is different from what has been reported for neutral sequences.<\/jats:p><jats:p>Availability: The Indelign program may be downloaded from the website<\/jats:p><jats:p>Supplementary information: Supplementary material is available at Bioinformatics online.<\/jats:p><jats:p>Contact: \u00a0sinhas@uiuc.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl578","type":"journal-article","created":{"date-parts":[[2006,11,17]],"date-time":"2006-11-17T01:17:37Z","timestamp":1163726257000},"page":"289-297","source":"Crossref","is-referenced-by-count":33,"title":["Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment"],"prefix":"10.1093","volume":"23","author":[{"given":"Jaebum","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Illinois, Urbana-Champaign \u00a0 Urbana, IL, USA"}]},{"given":"Saurabh","family":"Sinha","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Illinois, Urbana-Champaign \u00a0 Urbana, IL, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,11,15]]},"reference":[{"key":"2023041109272455900_","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1101\/gr.1933104","article-title":"Aligning multiple genomic sequences with the threaded blockset aligner","volume":"14","author":"Blanchette","year":"2004","journal-title":"Genome Res."},{"key":"2023041109272455900_","doi-asserted-by":"crossref","first-page":"2412","DOI":"10.1101\/gr.2800104","article-title":"Reconstructing large regions of an ancestral mammalian genome in silico","volume":"14","author":"Blanchette","year":"2004","journal-title":"Genome Res."},{"key":"2023041109272455900_","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1101\/gr.926603","article-title":"LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA","volume":"13","author":"Brudno","year":"2003","journal-title":"Genome Res."},{"key":"2023041109272455900_","doi-asserted-by":"crossref","first-page":"iii31","DOI":"10.1093\/bioinformatics\/bti1200","article-title":"DNA assembly with gaps (Dawg): simulating sequence evolution","volume":"21","author":"Cartwright","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041109272455900_","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: a maximum likelihood approach","volume":"17","author":"Felsenstein","year":"1981","journal-title":"J. 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