{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T22:57:20Z","timestamp":1762297040035},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Genomic mutations and variations provide insightful information about the functionality of sequence elements and their association with human diseases. Traditionally, variations are identified through analysis of short DNA sequences, usually shorter than 1000 bp per fragment. Optical maps provide both faster and more cost-efficient means for detecting such differences, because a single map can span over 1 million bp. Optical maps are assembled to cover the whole genome, and the accuracy of assembly is critical.<\/jats:p>\n               <jats:p>Results: We present a computationally efficient model-based method for improving quality of such assemblies. Our method provides very high accuracy even with moderate coverage (&amp;lt;20 \u00d7). We utilize a hidden Markov model to represent the consensus map and use the expectation-Maximization algorithm to drive the refinement process. We also provide quality scores to assess the quality of the finished map.<\/jats:p>\n               <jats:p>Availability: Code is available from<\/jats:p>\n               <jats:p>Contact: \u00a0valouev@usc.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl063","type":"journal-article","created":{"date-parts":[[2006,2,25]],"date-time":"2006-02-25T01:14:23Z","timestamp":1140830063000},"page":"1217-1224","source":"Crossref","is-referenced-by-count":26,"title":["Refinement of optical map assemblies"],"prefix":"10.1093","volume":"22","author":[{"given":"Anton","family":"Valouev","sequence":"first","affiliation":[{"name":"MCB 1 \u00a0 1 \u00a0 \u00a0 1050 Childs Way, Los Angeles, CA 90089-2910, USA"},{"name":"Department of Mathematics, University of Southern California 2 \u00a0 2 \u00a0 \u00a0 Los Angeles, CA, USA"}]},{"given":"Yu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Statistics, Harvard University 3 \u00a0 3 \u00a0 \u00a0 MA, USA"}]},{"given":"David C.","family":"Schwartz","sequence":"additional","affiliation":[{"name":"Laboratory for Molecular and Computational Genomics, Departments of Genetics and Chemistry, University of Wisconsin-Madison 4 \u00a0 4 \u00a0 \u00a0 WI, USA"}]},{"given":"Michael S.","family":"Waterman","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of Southern California 2 \u00a0 2 \u00a0 \u00a0 Los Angeles, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,2,24]]},"reference":[{"key":"2023012408202176000_b1","article-title":"Genomics via optical mapping III: contiging genomic DNA and variations","author":"Ananthraman","year":"1999"},{"key":"2023012408202176000_b2","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/S0888-7543(05)80288-5","article-title":"The accuracy of DNA sequences: estimating sequence quality","volume":"14","author":"Churchill","year":"1992","journal-title":"Genomics"},{"key":"2023012408202176000_b3","doi-asserted-by":"crossref","first-page":"5293","DOI":"10.1021\/ac0496401","article-title":"A microfluidic system for large DNA molecule arrays","volume":"76","author":"Dimalanta","year":"2004","journal-title":"Anal. 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