{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T04:40:51Z","timestamp":1721191251541},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":139,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs.<\/jats:p>\n               <jats:p>Results: We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5\u2032-end processing and 3\u2032-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain.<\/jats:p>\n               <jats:p>Availability and Implementation: The source code of our program SHARAKU is available at http:\/\/www.dna.bio.keio.ac.jp\/sharaku\/ , and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502.<\/jats:p>\n               <jats:p>Contact: \u00a0yasu@bio.keio.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw273","type":"journal-article","created":{"date-parts":[[2016,6,15]],"date-time":"2016-06-15T15:43:52Z","timestamp":1466005432000},"page":"i369-i377","source":"Crossref","is-referenced-by-count":3,"title":["SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing"],"prefix":"10.1093","volume":"32","author":[{"given":"Mariko","family":"Tsuchiya","sequence":"first","affiliation":[{"name":"Department of Biosciences and Informatics, Keio University, Yokohama 161-0031, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kojiro","family":"Amano","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Informatics, Keio University, Yokohama 161-0031, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masaya","family":"Abe","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Informatics, Keio University, Yokohama 161-0031, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Misato","family":"Seki","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Informatics, Keio University, Yokohama 161-0031, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sumitaka","family":"Hase","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Informatics, Keio University, Yokohama 161-0031, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kengo","family":"Sato","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Informatics, Keio University, Yokohama 161-0031, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasubumi","family":"Sakakibara","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Informatics, Keio University, Yokohama 161-0031, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,6,11]]},"reference":[{"key":"2023020112341227100_btw273-B1","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.ymeth.2013.05.001","article-title":"Small RNAs derived from structural non-coding RNAs","volume":"63","author":"Chen","year":"2013","journal-title":"Methods"},{"key":"2023020112341227100_btw273-B2","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids","author":"Durbin","year":"1998"},{"key":"2023020112341227100_btw273-B3","doi-asserted-by":"crossref","first-page":"i426","DOI":"10.1093\/bioinformatics\/btq363","article-title":"Classification of ncRNAs using position and size information in deep sequencing data","volume":"26","author":"Erhard","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020112341227100_btw273-B4","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1261\/rna.2000810","article-title":"Human tRNA-derived small RNAs in the global regulation of RNA silencing","volume":"16","author":"Haussecker","year":"2010","journal-title":"RNA"},{"key":"2023020112341227100_btw273-B5","first-page":"955","article-title":"Vienna RNA secondary structure server","volume":"25","author":"Hofacker","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2023020112341227100_btw273-B6","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1093\/bioinformatics\/btu696","article-title":"FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data","volume":"31","author":"Hoogstrate","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020112341227100_btw273-B7","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1016\/j.cell.2009.01.019","article-title":"The many pathways of RNA degradation","volume":"136","author":"Houseley","year":"2009","journal-title":"Cell"},{"key":"2023020112341227100_btw273-B8","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/1471-2164-9-157","article-title":"Hidden layers of human small RNAs","volume":"9","author":"Kawaji","year":"2008","journal-title":"BMC Genomics"},{"key":"2023020112341227100_btw273-B9","doi-asserted-by":"crossref","first-page":"2298","DOI":"10.1093\/bioinformatics\/btp419","article-title":"Evidence for human microRNA-offset RNAs in small RNA sequencing data","volume":"25","author":"Langenberger","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020112341227100_btw273-B10","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1093\/bioinformatics\/btr598","article-title":"deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns","volume":"28","author":"Langenberger","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020112341227100_btw273-B11","doi-asserted-by":"crossref","first-page":"2639","DOI":"10.1101\/gad.1837609","article-title":"A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)","volume":"23","author":"Lee","year":"2009","journal-title":"Genes Dev"},{"key":"2023020112341227100_btw273-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":"2023020112341227100_btw273-B13","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023020112341227100_btw273-B14","first-page":"12062","article-title":"The common Marmoset genome provides insight into primate biology and evolution","volume":"5","author":"Marmoset Genome Sequencing and Analysis Consortium","year":"2014","journal-title":"Nat. Genet"},{"key":"2023020112341227100_btw273-B15","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.canlet.2012.11.058","article-title":"Beyond microRNA\u2013novel RNAs derived from small non-coding RNA and their implication in cancer","volume":"340","author":"Martens-Uzunova","year":"2013","journal-title":"Cancer Lett"},{"key":"2023020112341227100_btw273-B16","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1002\/bip.360290621","article-title":"The equilibrium partition function and base pair binding probabilities for RNA secondary structure","volume":"29","author":"McCaskill","year":"1990","journal-title":"Biopolymers"},{"key":"2023020112341227100_btw273-B17","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1093\/nar\/gkn1054","article-title":"Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans","volume":"37","author":"Morita","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023020112341227100_btw273-B18","doi-asserted-by":"crossref","first-page":"3879","DOI":"10.1093\/nar\/gkq1355","article-title":"Identification of human miRNA precursors that resemble box C\/D snoRNAs","volume":"39","author":"Ono","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023020112341227100_btw273-B19","doi-asserted-by":"crossref","first-page":"12062.","DOI":"10.1038\/srep12062","article-title":"Differential and coherent processing patterns from small RNAs","volume":"5","author":"Pundhir","year":"2015","journal-title":"Sci. Rep"},{"key":"2023020112341227100_btw273-B20","doi-asserted-by":"crossref","first-page":"188","DOI":"10.3389\/fgene.2015.00188","article-title":"Emerging applications of read profiles towards the functional annotation of the genome","volume":"6","author":"Pundhir","year":"2015","journal-title":"Front. Genet"},{"key":"2023020112341227100_btw273-B21","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1093\/bioinformatics\/bth141","article-title":"Protein homology detection using string alignment kernels","volume":"20","author":"Saigo","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020112341227100_btw273-B22","doi-asserted-by":"crossref","first-page":"3218","DOI":"10.1093\/bioinformatics\/bts612","article-title":"DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition","volume":"28","author":"Sato","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020112341227100_btw273-B23","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1016\/j.biochi.2011.05.026","article-title":"From snoRNA to miRNA: Dual function regulatory non-coding RNAs","volume":"93","author":"Scott","year":"2011","journal-title":"Biochimie"},{"key":"2023020112341227100_btw273-B24","doi-asserted-by":"crossref","first-page":"3676","DOI":"10.1093\/nar\/gkr1233","article-title":"Human box C\/D snoRNA processing conservation across multiple cell types","volume":"40","author":"Scott","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023020112341227100_btw273-B25","first-page":"1987","article-title":"Transfer RNA-derived fragments: origins, processing, and functions","volume":"93","author":"Sobala","year":"2011","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"2023020112341227100_btw273-B26","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1261\/rna.1528909","article-title":"Small RNAs derived from snoRNAs","volume":"15","author":"Taft","year":"2009","journal-title":"RNA"},{"key":"2023020112341227100_btw273-B27","doi-asserted-by":"crossref","first-page":"i274","DOI":"10.1093\/bioinformatics\/btu270","article-title":"BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles","volume":"30","author":"Videm","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020112341227100_btw273-B28","doi-asserted-by":"crossref","first-page":"e65","DOI":"10.1371\/journal.pcbi.0030065","article-title":"Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering","volume":"3","author":"Will","year":"2007","journal-title":"PLoS Comput. Biol"},{"key":"2023020112341227100_btw273-B29","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1083\/jcb.200811106","article-title":"Angiogenin cleaves tRNA and promotes stress-induced translational repression","volume":"185","author":"Yamasaki","year":"2009","journal-title":"J. Cell. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/12\/i369\/49020089\/bioinformatics_32_12_i369.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/12\/i369\/49020089\/bioinformatics_32_12_i369.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:46:07Z","timestamp":1675291567000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/12\/i369\/2288858"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,6,11]]},"references-count":29,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2016,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw273","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,6,15]]},"published":{"date-parts":[[2016,6,11]]}}}