{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,6]],"date-time":"2025-06-06T14:49:00Z","timestamp":1749221340065},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1795,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput sequencing methods allow whole transcriptomes to be sequenced fast and cost-effectively. Short RNA sequencing provides not only quantitative expression data but also an opportunity to identify novel coding and non-coding RNAs. Many long transcripts undergo post-transcriptional processing that generates short RNA sequence fragments. Mapped back to a reference genome, they form distinctive patterns that convey information on both the structure of the parent transcript and the modalities of its processing. The miR-miR* pattern from microRNA precursors is the best-known, but by no means singular, example.<\/jats:p>\n               <jats:p>Results: \u00a0deepBlockAlign introduces a two-step approach to align RNA-seq read patterns with the aim of quickly identifying RNAs that share similar processing footprints. Overlapping mapped reads are first merged to blocks and then closely spaced blocks are combined to block groups, each representing a locus of expression. In order to compare block groups, the constituent blocks are first compared using a modified sequence alignment algorithm to determine similarity scores for pairs of blocks. In the second stage, block patterns are compared by means of a modified Sankoff algorithm that takes both block similarities and similarities of pattern of distances within the block groups into account. Hierarchical clustering of block groups clearly separates most miRNA and tRNA, and also identifies about a dozen tRNAs clustering together with miRNA. Most of these putative Dicer-processed tRNAs, including eight cases reported to generate products with miRNA-like features in literature, exhibit read blocks distinguished by precise start position of reads.<\/jats:p>\n               <jats:p>Availability: The program deepBlockAlign is available as source code from http:\/\/rth.dk\/resources\/dba\/.<\/jats:p>\n               <jats:p>Contact: \u00a0gorodkin@rth.dk; studla@bioinf.uni-leipzig.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr598","type":"journal-article","created":{"date-parts":[[2011,11,4]],"date-time":"2011-11-04T01:43:06Z","timestamp":1320370986000},"page":"17-24","source":"Crossref","is-referenced-by-count":17,"title":["deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns"],"prefix":"10.1093","volume":"28","author":[{"given":"David","family":"Langenberger","sequence":"first","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"},{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"}]},{"given":"Sachin","family":"Pundhir","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"},{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"}]},{"given":"Claus T.","family":"Ekstr\u00f8m","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"},{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"},{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"},{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"},{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"},{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"},{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"}]},{"given":"Steve","family":"Hoffmann","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"},{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"}]},{"given":"Jan","family":"Gorodkin","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"},{"name":"1 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, 2Transcriptome Bioinformatics group, LIFE - Leipzig Research Center for Civilization Diseases, Universit\u00e4t Leipzig, Philipp-Rosenthal-Strasse 27, D-04107 Leipzig, Germany, 3Center for non-coding RNA in Technology and Health, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 4Center for Applied Bioinformatics, Department of Basic Animal and Veterinary Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark, 5Center for Applied Bioinformatics, Department of Basic Sciences and Environment, University of Copenhagen, 1871 Frederiksberg C, Denmark, 6Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, 7RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany, 8Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Vienna, Austria and 9The Santa Fe"}]}],"member":"286","published-online":{"date-parts":[[2011,11,3]]},"reference":[{"key":"2023061011450928100_B1","article-title":"Fast Sequence Alignment in a Managed Programming Language","volume-title":"Master's Thesis","author":"Akbasli","year":"2007"},{"key":"2023061011450928100_B2","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1471-2199-12-6","article-title":"Two-step cleavage of hairpin RNA with 5\u2032overhangs by human DICER","volume":"12","author":"Ando","year":"2011","journal-title":"BMC Mol. Biol."},{"key":"2023061011450928100_B3","doi-asserted-by":"crossref","first-page":"2773","DOI":"10.1101\/gad.1705308","article-title":"Mouse es cells express endogenous shrnas, sirnas, and other microprocessor-independent, dicer-dependent small rnas","volume":"22","author":"Babiarz","year":"2008","journal-title":"Genes Dev."},{"key":"2023061011450928100_B4","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1093\/nar\/gkq776","article-title":"Human box C\/D snornas with miRNA like functions: expanding the range of regulatory RNAs","volume":"39","author":"Brameier","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023061011450928100_B5","first-page":"1","article-title":"clValid: an R package for cluster validation","volume":"25","author":"Brock","year":"2008","journal-title":"J. Stat. Softwr."},{"key":"2023061011450928100_B6","doi-asserted-by":"crossref","first-page":"158","DOI":"10.4161\/rna.8.1.14300","article-title":"Deep-sequencing of human argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin","volume":"8","author":"Burroughs","year":"2011","journal-title":"RNA Biol."},{"key":"2023061011450928100_B7","doi-asserted-by":"crossref","first-page":"18097","DOI":"10.1073\/pnas.0709193104","article-title":"RNA sequence analysis defines Dicer's role in mouse embryonic stem cells","volume":"104","author":"Calabrese","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023061011450928100_B8","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1089\/106652704773416876","article-title":"1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap","volume":"11","author":"Caprara","year":"2004","journal-title":"J. Comput. Biol."},{"key":"2023061011450928100_B9","doi-asserted-by":"crossref","first-page":"D93","DOI":"10.1093\/nar\/gkn787","article-title":"GtRNAdb: a database of transfer RNA genes detected in genomic sequence","volume":"37","author":"Chan","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023061011450928100_B10","doi-asserted-by":"crossref","first-page":"1694","DOI":"10.1126\/science.1190809","article-title":"A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity","volume":"328","author":"Cifuentes","year":"2010","journal-title":"Science"},{"key":"2023061011450928100_B11","doi-asserted-by":"crossref","first-page":"2147","DOI":"10.1261\/rna.1738409","article-title":"Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs","volume":"15","author":"Cole","year":"2009","journal-title":"RNA"},{"key":"2023061011450928100_B12","doi-asserted-by":"crossref","first-page":"3704","DOI":"10.1093\/bioinformatics\/bti616","article-title":"Pairwise alignment incorporating dipeptide covariation","volume":"21","author":"Crooks","year":"2005","journal-title":"Bioinformatics"},{"key":"2023061011450928100_B13","first-page":"95","article-title":"Well-separated clusters and optimal fuzzy partitions","volume":"4","author":"Dunn","year":"1974","journal-title":"Cybern. Syst."},{"key":"2023061011450928100_B14","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":"2023061011450928100_B15","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1515\/bc.2011.043","article-title":"Traces of post-transcriptional RNA modifications in deep sequencing data","volume":"392","author":"Findei\u00df","year":"2011","journal-title":"Biol. Chem."},{"key":"2023061011450928100_B16","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1111\/j.1365-2958.2007.06032.x","article-title":"A stepwise model for double-stranded RNA processing by ribonuclease III","volume":"67","author":"Gan","year":"2008","journal-title":"Mol. Microbiol."},{"key":"2023061011450928100_B17","doi-asserted-by":"crossref","first-page":"e1002100","DOI":"10.1371\/journal.pcbi.1002100","article-title":"From structure prediction to genomic screens for novel non-coding RNAs","volume":"7","author":"Gorodkin","year":"2011","journal-title":"PLoS Comput. Biol."},{"key":"2023061011450928100_B18","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.tibtech.2009.09.006","article-title":"De novo prediction of structured RNAs from genomic sequences","volume":"28","author":"Gorodkin","year":"2010","journal-title":"Trends Biotech."},{"key":"2023061011450928100_B19","doi-asserted-by":"crossref","first-page":"3201","DOI":"10.1093\/bioinformatics\/bti517","article-title":"Computational cluster validation in post-genomic data analysis","volume":"21","author":"Handl","year":"2005","journal-title":"Bioinformatics"},{"key":"2023061011450928100_B20","doi-asserted-by":"crossref","first-page":"e131","DOI":"10.1093\/nar\/gkq224","article-title":"Biases in illumina transcriptome sequencing caused by random hexamer priming","volume":"38","author":"Hansen","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023061011450928100_B21","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":"2023061011450928100_B22","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gkj144","article-title":"The UCSC genome browser database: update 2006","volume":"34","author":"Hinrichs","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023061011450928100_B23","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/BF00818163","article-title":"Fast folding and comparison of RNA secondary structures","volume":"125","author":"Hofacker","year":"1994","journal-title":"Chem. Month."},{"key":"2023061011450928100_B24","doi-asserted-by":"crossref","first-page":"e1000502","DOI":"10.1371\/journal.pcbi.1000502","article-title":"Fast mapping of short sequences with mismatches, insertions and deletions using index structures","volume":"5","author":"Hoffmann","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023061011450928100_B25","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/1471-2164-11-77","article-title":"Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data","volume":"11","author":"Jung","year":"2010","journal-title":"BMC Genomics"},{"key":"2023061011450928100_B26","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1093\/bioinformatics\/btn628","article-title":"Structural profiles of human miRNA families from pairwise clustering","volume":"25","author":"Kaczkowski","year":"2009","journal-title":"Bioinformatics"},{"key":"2023061011450928100_B27","doi-asserted-by":"crossref","first-page":"D493","DOI":"10.1093\/nar\/gkh103","article-title":"The UCSC table browser data retrieval tool","volume":"32","author":"Karolchik","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023061011450928100_B28","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":"2023061011450928100_B29","doi-asserted-by":"crossref","first-page":"D152","DOI":"10.1093\/nar\/gkq1027","article-title":"miRBase: integrating microRNA annotation and deep-sequencing data","volume":"39","author":"Kozomara","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023061011450928100_B30","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":"2023061011450928100_B31","first-page":"80","article-title":"Identification and classification of small RNAs in transcriptome sequence data","volume":"15","author":"Langenberger","year":"2010","journal-title":"Pacific Symposium Biocomputing"},{"key":"2023061011450928100_B32","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023061011450928100_B33","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":"2023061011450928100_B34","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-5-r50","article-title":"Method modeling non-uniformity in short-read rates in rna-seq data","volume":"11","author":"Li","year":"2010","journal-title":"Genome Biol."},{"key":"2023061011450928100_B35","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1101\/gr.110189.110","article-title":"Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data","volume":"21","author":"Lu","year":"2011","journal-title":"Genome Res."},{"key":"2023061011450928100_B36","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1007\/s00438-010-0556-1","article-title":"Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production","volume":"284","author":"Miyoshi","year":"2010","journal-title":"Mol. Genet. Genomics"},{"key":"2023061011450928100_B37","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1101\/gr.7179508","article-title":"Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells","volume":"18","author":"Morin","year":"2008","journal-title":"Genome Res."},{"key":"2023061011450928100_B38","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","article-title":"A general method applicable to the search for similarities in the amino acid sequence of two proteins","volume":"48","author":"Needleman","year":"1970","journal-title":"J. Mol. Biol."},{"key":"2023061011450928100_B39","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: a graphical aid to the interpretation and validation of cluster analysis","volume":"20","author":"Rousseeuw","year":"1987","journal-title":"J. Comput. Appl. Math."},{"key":"2023061011450928100_B40","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1137\/0145048","article-title":"Simultaneous solution of the RNA folding, alignment and protosequence problems","volume":"45","author":"Sankoff","year":"1985","journal-title":"SIAM J. Appl. Math."},{"key":"2023061011450928100_B41","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1038\/nsmb.1536","article-title":"A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate","volume":"16","author":"Shi","year":"2009","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023061011450928100_B42","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1101\/gr.106849.110","article-title":"MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain","volume":"20","author":"Somel","year":"2010","journal-title":"Genome Res."},{"key":"2023061011450928100_B43","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1101\/gad.1613108","article-title":"A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands","volume":"22","author":"Stark","year":"2008","journal-title":"Genes Dev."},{"key":"2023061011450928100_B44","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1093\/bioinformatics\/btl117","article-title":"Pvclust: an R package for assessing the uncertainty in hierarchical clustering","volume":"22","author":"Suzuki","year":"2006","journal-title":"Bioinformatics"},{"key":"2023061011450928100_B45","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":"2023061011450928100_B46","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"2023061011450928100_B47","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1038\/nmeth.1529","article-title":"FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing","volume":"7","author":"Underwood","year":"2010","journal-title":"Nat. Methods"},{"key":"2023061011450928100_B48","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."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/1\/17\/50568356\/bioinformatics_28_1_17.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/1\/17\/50568356\/bioinformatics_28_1_17.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T11:46:47Z","timestamp":1686397607000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/1\/17\/219213"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11,3]]},"references-count":48,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr598","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,1,1]]},"published":{"date-parts":[[2011,11,3]]}}}