{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:15:42Z","timestamp":1761743742902},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Simple tandem repeats are highly variable genetic elements and widespread in genomes of many organisms. Next-generation sequencing technologies have enabled a robust comparison of large numbers of simple tandem repeat loci; however, analysis of their variation using traditional sequence analysis approaches still remains limiting and problematic due to variants occurring in repeat sequences confusing alignment programs into mapping sequence reads to incorrect loci when the sequence reads are significantly different from the reference sequence.<\/jats:p><jats:p>Results: We have developed a program, ReviSTER, which is an automated pipeline using a \u2018local mapping reference reconstruction method\u2019 to revise mismapped or partially misaligned reads at simple tandem repeat loci. RevisSTER estimates alleles of repeat loci using a local alignment method and creates temporary local mapping reference sequences, and finally remaps reads to the local mapping references. Using this approach, ReviSTER was able to successfully revise reads misaligned to repeat loci from both simulated data and real data.<\/jats:p><jats:p>Availability: ReviSTER is open-source software available at http:\/\/revister.sourceforge.net.<\/jats:p><jats:p>Contact: \u00a0garner@vbi.vt.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt277","type":"journal-article","created":{"date-parts":[[2013,5,16]],"date-time":"2013-05-16T01:00:44Z","timestamp":1368666044000},"page":"1734-1741","source":"Crossref","is-referenced-by-count":12,"title":["ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats"],"prefix":"10.1093","volume":"29","author":[{"given":"Hongseok","family":"Tae","sequence":"first","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}]},{"given":"Kevin W.","family":"McMahon","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}]},{"given":"Robert E.","family":"Settlage","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}]},{"given":"Jasmin H.","family":"Bavarva","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}]},{"given":"Harold R.","family":"Garner","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,5,15]]},"reference":[{"key":"2023012810452870900_btt277-B1","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1101\/gr.112326.110","article-title":"Dindel: accurate indel calls from short-read data","volume":"21","author":"Albers","year":"2011","journal-title":"Genome Res."},{"key":"2023012810452870900_btt277-B2","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1038\/nrg798","article-title":"Alu repeats and human genomic diversity","volume":"3","author":"Batzer","year":"2002","journal-title":"Nat. Rev. Genet."},{"key":"2023012810452870900_btt277-B3","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":"2023012810452870900_btt277-B4","first-page":"746","article-title":"DNA typing and genetic mapping with trimeric and tetrameric tandem repeats","volume":"49","author":"Edwards","year":"1991","journal-title":"Am. J. Hum. Genet."},{"key":"2023012810452870900_btt277-B5","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1101\/gr.135780.111","article-title":"lobSTR: a short tandem repeat profiler for personal genomes","volume":"22","author":"Gymrek","year":"2012","journal-title":"Genome Res."},{"key":"2023012810452870900_btt277-B6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/oso\/9780198504085.003.0001","article-title":"Microsatellites and other simple sequences: genomic context and mutational mechanisms","volume-title":"Microsatellites: Evolution and applications","author":"HanCock","year":"1999"},{"key":"2023012810452870900_btt277-B7","doi-asserted-by":"crossref","first-page":"e32","DOI":"10.1093\/nar\/gks981","article-title":"Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles","volume":"41","author":"Highnam","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012810452870900_btt277-B8","doi-asserted-by":"crossref","first-page":"R99","DOI":"10.1186\/gb-2010-11-10-r99","article-title":"Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA","volume":"11","author":"Homer","year":"2010","journal-title":"Genome Biol."},{"key":"2023012810452870900_btt277-B9","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1093\/bioinformatics\/bts187","article-title":"pIRS: profile-based Illumina pair-end reads simulator","volume":"28","author":"Hu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012810452870900_btt277-B10","first-page":"656","article-title":"BLAT-the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012810452870900_btt277-B11","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"2023012810452870900_btt277-B12","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810452870900_btt277-B13","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810452870900_btt277-B14","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1101\/gr.132480.111","article-title":"SOAPindel: efficient identification of indels from short paired reads","volume":"23","author":"Li","year":"2013","journal-title":"Genome Res."},{"key":"2023012810452870900_btt277-B15","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nature10811","article-title":"The Drosophila melanogaster Genetic Reference Panel","volume":"482","author":"Mackay","year":"2012","journal-title":"Nature"},{"key":"2023012810452870900_btt277-B16","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/j.ygeno.2011.01.001","article-title":"Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments","volume":"97","author":"McIver","year":"2011","journal-title":"Genomics"},{"key":"2023012810452870900_btt277-B17","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"2023012810452870900_btt277-B18","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/nrg3295","article-title":"Revising the human mutation rate: implications for understanding human evolution","volume":"13","author":"Scally","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"2023012810452870900_btt277-B19","doi-asserted-by":"crossref","first-page":"6410","DOI":"10.1128\/JB.06181-11","article-title":"Revised genome sequence of Brucella suis 1330","volume":"193","author":"Tae","year":"2011","journal-title":"J. Bacteriol."},{"key":"2023012810452870900_btt277-B20","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1128\/JB.06556-11","article-title":"Complete genome sequence of Brucella suis VBI22, isolated from bovine milk","volume":"194","author":"Tae","year":"2012","journal-title":"J. Bacteriol."},{"key":"2023012810452870900_btt277-B21","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.ygeno.2012.07.015","article-title":"Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes","volume":"100","author":"Tae","year":"2012","journal-title":"Genomics"},{"key":"2023012810452870900_btt277-B22","doi-asserted-by":"crossref","first-page":"2865","DOI":"10.1093\/bioinformatics\/btp394","article-title":"Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads","volume":"25","author":"Ye","year":"2009","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/14\/1734\/48888521\/bioinformatics_29_14_1734.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/14\/1734\/48888521\/bioinformatics_29_14_1734.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T20:12:47Z","timestamp":1715371967000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/14\/1734\/231804"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,5,15]]},"references-count":22,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2013,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt277","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,7,15]]},"published":{"date-parts":[[2013,5,15]]}}}