{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T10:37:48Z","timestamp":1722681468378},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1759,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Deep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of colors, where each color represents 2 nt and each nucleotide is represented by two consecutive colors. This strategy is purported to have several advantages, including increased ability to distinguish sequencing errors from polymorphisms. Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issues arise when using SOLiD technology to characterize microRNAs.<\/jats:p>\n               <jats:p>Results: Here we explore these technical difficulties. First, since the sequenced reads are longer than the biological sequences, every read is expected to contain linker fragments. The color-calling error rate increases toward the 3\u2032 end of the read such that recognizing the linker sequence for removal becomes problematic. Second, mapping in color space may lead to the loss of the first nucleotide of each read. We propose a sequential trimming and mapping approach to map small RNAs. Using our strategy, we reanalyze three published insect small RNA deep sequencing datasets and characterize 22 new microRNAs.<\/jats:p>\n               <jats:p>Availability and implementation: A bash shell script to perform the sequential trimming and mapping procedure, called SeqTrimMap, is available at: http:\/\/www.mirbase.org\/tools\/seqtrimmap\/<\/jats:p>\n               <jats:p>Contact: antonio.marco@manchester.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr686","type":"journal-article","created":{"date-parts":[[2011,12,11]],"date-time":"2011-12-11T01:23:20Z","timestamp":1323566600000},"page":"318-323","source":"Crossref","is-referenced-by-count":17,"title":["Detection of microRNAs in color space"],"prefix":"10.1093","volume":"28","author":[{"given":"Antonio","family":"Marco","sequence":"first","affiliation":[{"name":"Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, M13 9PT Manchester, UK"}]},{"given":"Sam","family":"Griffiths-Jones","sequence":"additional","affiliation":[{"name":"Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, M13 9PT Manchester, UK"}]}],"member":"286","published-online":{"date-parts":[[2011,12,9]]},"reference":[{"key":"2023012512143484600_B1","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012512143484600_B2","author":"Applied","year":"2008","journal-title":"Principles of Di-base Sequencing and the Advantages of Color Space Analysis in the SOLiD System."},{"key":"2023012512143484600_B3","author":"Applied","year":"2009","journal-title":"SOLiD3 System Application Documentation Small RNA Analysis Tool."},{"key":"2023012512143484600_B4","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/S0092-8674(04)00045-5","article-title":"MicroRNAs: genomics, biogenesis, mechanism, and function","volume":"116","author":"Bartel","year":"2004","journal-title":"Cell"},{"key":"2023012512143484600_B5","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1101\/gr.116657.110","article-title":"Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence","volume":"21","author":"Berezikov","year":"2011","journal-title":"Genome Res."},{"key":"2023012512143484600_B6","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1007\/s10142-010-0162-7","article-title":"Novel microRNAs in silkworm (Bombyx mori)","volume":"10","author":"Cai","year":"2010","journal-title":"Funct. 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