{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T16:18:46Z","timestamp":1722701926298},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Tandem mass spectrometry has become a standard tool for identifying post-translational modifications (PTMs) of proteins. Algorithmic searches for PTMs from tandem mass spectrum data (MS\/MS) tend to be hampered by noisy data as well as by a combinatorial explosion of search space. This leads to high uncertainty and long search-execution times.<\/jats:p><jats:p>Results: To address this issue, we present PTMTreeSearch, a new algorithm that uses a large database of known PTMs to identify PTMs from MS\/MS data. For a given peptide sequence, PTMTreeSearch builds a computational tree wherein each path from the root to the leaves is labeled with the amino acids of a peptide sequence. Branches then represent PTMs. Various empirical tree pruning rules have been designed to decrease the search-execution time by eliminating biologically unlikely solutions. PTMTreeSearch first identifies a relatively small set of high confidence PTM types, and in a second stage, performs a more exhaustive search on this restricted set using relaxed search parameter settings. An analysis of experimental data shows that using the same criteria for false discovery, PTMTreeSearch annotates more peptides than the current state-of-the-art methods and PTM identification algorithms, and achieves this at roughly the same execution time. PTMTreeSearch is implemented as a plugable scoring function in the X!Tandem search engine.<\/jats:p><jats:p>Availability: The source code of PTMTreeSearch and a demo server application can be found at http:\/\/net.icgeb.org\/ptmtreesearch.<\/jats:p><jats:p>Contacts: \u00a0pongor@icgeb.org<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary materials are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt642","type":"journal-article","created":{"date-parts":[[2013,11,10]],"date-time":"2013-11-10T01:09:20Z","timestamp":1384045760000},"page":"234-241","source":"Crossref","is-referenced-by-count":4,"title":["PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS\/MS spectra"],"prefix":"10.1093","volume":"30","author":[{"given":"Attila","family":"Kert\u00e9sz-Farkas","sequence":"first","affiliation":[{"name":"1 Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, 99 Padriciano, Trieste, Italy, 34149, 2Institute of Biophysics, Biological Research Centre, Temesvari krt. 62, H-6727 Szeged, Hungary, 3Protein Networks Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, Padriciano 99, 34149 Trieste, Italy and 4Faculty of Information Technology, P\u00e1zm\u00e1ny P\u00e9ter Catholic University, Pr\u00e1ter u. 50\/a, H-1083 Budapest, Hungary"}]},{"given":"Be\u00e1ta","family":"Reiz","sequence":"additional","affiliation":[{"name":"1 Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, 99 Padriciano, Trieste, Italy, 34149, 2Institute of Biophysics, Biological Research Centre, Temesvari krt. 62, H-6727 Szeged, Hungary, 3Protein Networks Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, Padriciano 99, 34149 Trieste, Italy and 4Faculty of Information Technology, P\u00e1zm\u00e1ny P\u00e9ter Catholic University, Pr\u00e1ter u. 50\/a, H-1083 Budapest, Hungary"}]},{"given":"Roberto","family":"Vera","sequence":"additional","affiliation":[{"name":"1 Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, 99 Padriciano, Trieste, Italy, 34149, 2Institute of Biophysics, Biological Research Centre, Temesvari krt. 62, H-6727 Szeged, Hungary, 3Protein Networks Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, Padriciano 99, 34149 Trieste, Italy and 4Faculty of Information Technology, P\u00e1zm\u00e1ny P\u00e9ter Catholic University, Pr\u00e1ter u. 50\/a, H-1083 Budapest, Hungary"}]},{"given":"Michael P.","family":"Myers","sequence":"additional","affiliation":[{"name":"1 Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, 99 Padriciano, Trieste, Italy, 34149, 2Institute of Biophysics, Biological Research Centre, Temesvari krt. 62, H-6727 Szeged, Hungary, 3Protein Networks Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, Padriciano 99, 34149 Trieste, Italy and 4Faculty of Information Technology, P\u00e1zm\u00e1ny P\u00e9ter Catholic University, Pr\u00e1ter u. 50\/a, H-1083 Budapest, Hungary"}]},{"given":"S\u00e1ndor","family":"Pongor","sequence":"additional","affiliation":[{"name":"1 Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, 99 Padriciano, Trieste, Italy, 34149, 2Institute of Biophysics, Biological Research Centre, Temesvari krt. 62, H-6727 Szeged, Hungary, 3Protein Networks Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, Padriciano 99, 34149 Trieste, Italy and 4Faculty of Information Technology, P\u00e1zm\u00e1ny P\u00e9ter Catholic University, Pr\u00e1ter u. 50\/a, H-1083 Budapest, Hungary"},{"name":"1 Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, 99 Padriciano, Trieste, Italy, 34149, 2Institute of Biophysics, Biological Research Centre, Temesvari krt. 62, H-6727 Szeged, Hungary, 3Protein Networks Group, International Centre for Genetic Engineering and Biotechnology, AREA Research Park, Padriciano 99, 34149 Trieste, Italy and 4Faculty of Information Technology, P\u00e1zm\u00e1ny P\u00e9ter Catholic University, Pr\u00e1ter u. 50\/a, H-1083 Budapest, Hungary"}]}],"member":"286","published-online":{"date-parts":[[2013,11,8]]},"reference":[{"key":"2023012710385422700_btt642-B1","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1038\/nature01511","article-title":"Mass spectrometry-based proteomics","volume":"422","author":"Aebersold","year":"2003","journal-title":"Nature"},{"key":"2023012710385422700_btt642-B2","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/pmic.200900502","article-title":"Unrestricted identification of modified proteins using MS\/MS","volume":"10","author":"Ahrne","year":"2010","journal-title":"Proteomics"},{"key":"2023012710385422700_btt642-B3","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1074\/mcp.M900487-MCP200","article-title":"A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry","volume":"9","author":"Baliban","year":"2010","journal-title":"Mol Cell Proteom."},{"key":"2023012710385422700_btt642-B4","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.mrgentox.2010.06.016","article-title":"Recent developments in quantitative proteomics","volume":"722","author":"Becker","year":"2011","journal-title":"Mutation Res."},{"key":"2023012710385422700_btt642-B5","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. Royal Stat. Soc. Series B (Methodological)"},{"key":"2023012710385422700_btt642-B6","doi-asserted-by":"crossref","first-page":"3481","DOI":"10.1021\/pr800217q","article-title":"Conjugation of complex polyubiquitin chains to WRNIP1","volume":"7","author":"Bish","year":"2008","journal-title":"J. Proteome Res."},{"key":"2023012710385422700_btt642-B53","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1021\/pr0701198","article-title":"X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers","volume":"7","author":"Bjornson","year":"2008","journal-title":"J. Proteome Res."},{"key":"2023012710385422700_btt642-B7","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1073\/pnas.0811739106","article-title":"PTMap\u2014a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites","volume":"106","author":"Chen","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012710385422700_btt642-B8","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1109\/ICBBT.2010.5478968","article-title":"Unrestricted identification of post translational modifications from tandem mass spectra datasets","volume-title":"Proceedings of the International Conference on Bioinformatics and Biomedical Technology (ICBBT), 2010, Sanya, China","author":"Chiyong","year":"2010"},{"key":"2023012710385422700_btt642-B9","first-page":"797","article-title":"Computational refinement of post-translational modifications predicted from tandem mass spectrometry","volume":"27","author":"Chung","year":"2011","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023012710385422700_btt642-B10","doi-asserted-by":"crossref","first-page":"2310","DOI":"10.1002\/rcm.1198","article-title":"A method for reducing the time required to match protein sequences with tandem mass spectra","volume":"17","author":"Craig","year":"2003","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"2023012710385422700_btt642-B11","first-page":"1466","article-title":"TANDEM: matching proteins with tandem mass spectra","volume":"20","author":"Craig","year":"2004","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023012710385422700_btt642-B12","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1021\/pr049882h","article-title":"Open source system for analyzing, validating, and storing protein identification data","volume":"3","author":"Craig","year":"2004","journal-title":"J. Proteome Res."},{"key":"2023012710385422700_btt642-B13","doi-asserted-by":"crossref","first-page":"1426","DOI":"10.1002\/1615-9861(200210)2:10<1426::AID-PROT1426>3.0.CO;2-5","article-title":"Error tolerant searching of uninterpreted tandem mass spectrometry data","volume":"2","author":"Creasy","year":"2002","journal-title":"Proteomics"},{"key":"2023012710385422700_btt642-B14","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1152\/physiolgenomics.00298.2007","article-title":"Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics","volume":"33","author":"Deutsch","year":"2008","journal-title":"Physiol. Genom."},{"key":"2023012710385422700_btt642-B15","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nmeth1019","article-title":"Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry","volume":"4","author":"Elias","year":"2007","journal-title":"Nat. Methods"},{"key":"2023012710385422700_btt642-B16","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1016\/j.jasms.2007.01.010","article-title":"Validated MALDI-TOF\/TOF mass spectra for protein standards","volume":"18","author":"Falkner","year":"2007","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2023012710385422700_btt642-B17","doi-asserted-by":"crossref","first-page":"M110 000455","DOI":"10.1074\/mcp.M110.000455","article-title":"DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS\/MS data","volume":"10","author":"Fu","year":"2011","journal-title":"Mol. Cell Proteom."},{"key":"2023012710385422700_btt642-B18","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1093\/nar\/gkg038","article-title":"The RESID database of protein modifications: 2003 developments","volume":"31","author":"Garavelli","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012710385422700_btt642-B19","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1021\/pr0499491","article-title":"Open mass spectrometry search algorithm","volume":"3","author":"Geer","year":"2004","journal-title":"J. Proteome Res."},{"key":"2023012710385422700_btt642-B20","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1038\/msb.2008.75","article-title":"An integrated workflow for charting the human interaction proteome: insights into the PP2A system","volume":"5","author":"Glatter","year":"2009","journal-title":"Mol. Syst. Biol."},{"key":"2023012710385422700_btt642-B21","volume-title":"Signal Detection Theory and Psychophysics","author":"Green","year":"1966"},{"key":"2023012710385422700_btt642-B22","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1021\/pr0498234","article-title":"P-Mod: an algorithm and software to map modifications to peptide sequences using tandem MS data","volume":"4","author":"Hansen","year":"2005","journal-title":"J. Proteome Res."},{"key":"2023012710385422700_btt642-B23","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1109\/TSSC.1968.300136","article-title":"A formal basis for the heuristic determination of minimum cost paths","volume":"4","author":"Hart","year":"1968","journal-title":"Systems Science and Cybernetics"},{"key":"2023012710385422700_btt642-B24","doi-asserted-by":"crossref","first-page":"1362","DOI":"10.1021\/ac061515x","article-title":"Large-scale unrestricted identification of post-translation modifications using tandem mass spectrometry","volume":"79","author":"Havilio","year":"2007","journal-title":"Anal. Chem."},{"key":"2023012710385422700_btt642-B25","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1007\/978-1-60761-780-8_4","article-title":"Bioinformatics for LC-MS\/MS-based proteomics","volume":"658","author":"Jacob","year":"2010","journal-title":"Methods Mol. Biol."},{"key":"2023012710385422700_btt642-B26","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-13-S16-S2","article-title":"False discovery rates in spectral identification","volume":"13","author":"Jeong","year":"2012","journal-title":"BMC Bioinform."},{"key":"2023012710385422700_btt642-B27","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.ymeth.2004.08.014","article-title":"Informatics for protein identification by mass spectrometry","volume":"35","author":"Johnson","year":"2005","journal-title":"Methods"},{"key":"2023012710385422700_btt642-B28","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1021\/pr700600n","article-title":"Assigning significance to peptides identified by tandem mass spectrometry using decoy databases","volume":"7","author":"Kall","year":"2007","journal-title":"J. Proteome Res."},{"key":"2023012710385422700_btt642-B29","doi-asserted-by":"crossref","first-page":"1985","DOI":"10.1002\/pmic.200300721","article-title":"The International Protein Index: an integrated database for proteomics experiments","volume":"4","author":"Kersey","year":"2004","journal-title":"Proteomics"},{"key":"2023012710385422700_btt642-B30","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-23783-6_11","article-title":"PTMSearch: a greedy tree traversal algorithm for finding protein post-translational modifications in tandem mass spectra","volume-title":"Proceedings of the 2011 European conference on Machine Learning and Knowledge Discovery in Databases - Volume Part II","author":"Kertesz-Farkas","year":"2011"},{"key":"2023012710385422700_btt642-B31","doi-asserted-by":"crossref","first-page":"221","DOI":"10.2174\/157489312800604354","article-title":"Database searching in mass spectrometry based proteomics","volume":"7","author":"Kertesz-Farkas","year":"2012","journal-title":"Curr. Bioinform."},{"key":"2023012710385422700_btt642-B32","doi-asserted-by":"crossref","first-page":"8387","DOI":"10.1021\/ac901163c","article-title":"PTMSearchPlus: software tool for automated protein identification and post-translational modification characterization by integrating accurate intact protein mass and bottom-up mass spectrometric data searches","volume":"81","author":"Kertesz","year":"2009","journal-title":"Anal. Chem."},{"key":"2023012710385422700_btt642-B33","doi-asserted-by":"crossref","first-page":"W258","DOI":"10.1093\/nar\/gkl245","article-title":"MODi: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra","volume":"34","author":"Kim","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012710385422700_btt642-B34","doi-asserted-by":"crossref","first-page":"7846","DOI":"10.1021\/ac8009017","article-title":"Sequential interval motif search: unrestricted database surveys of global MS\/MS data sets for detection of putative post-translational modifications","volume":"80","author":"Liu","year":"2008","journal-title":"Anal. Chem."},{"key":"2023012710385422700_btt642-B35","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.cbpa.2004.12.010","article-title":"Computational analysis of shotgun proteomics data","volume":"9","author":"MacCoss","year":"2005","journal-title":"Curr. Opin. Chem. Biol."},{"key":"2023012710385422700_btt642-B36","doi-asserted-by":"crossref","first-page":"7900","DOI":"10.1073\/pnas.122231399","article-title":"Shotgun identification of protein modifications from protein complexes and lens tissue","volume":"99","author":"MacCoss","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012710385422700_btt642-B37","doi-asserted-by":"crossref","first-page":"2830","DOI":"10.1093\/bioinformatics\/btl379","article-title":"General framework for developing and evaluating database scoring algorithms using the TANDEM search engine","volume":"22","author":"MacLean","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012710385422700_btt642-B38","doi-asserted-by":"crossref","first-page":"2162","DOI":"10.1002\/rcm.1603","article-title":"MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications","volume":"18","author":"McDonald","year":"2004","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"2023012710385422700_btt642-B39","doi-asserted-by":"crossref","first-page":"2051","DOI":"10.1021\/pr900929m","article-title":"Peptidomics coming of age: a review of contributions from a bioinformatics angle","volume":"9","author":"Menschaert","year":"2010","journal-title":"J. Proteome Res."},{"key":"2023012710385422700_btt642-B40","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1016\/S1044-0305(02)00352-5","article-title":"Qscore: an algorithm for evaluating SEQUEST database search results","volume":"13","author":"Moore","year":"2002","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2023012710385422700_btt642-B41","doi-asserted-by":"crossref","first-page":"2092","DOI":"10.1016\/j.jprot.2010.08.009","article-title":"A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics","volume":"73","author":"Nesvizhskii","year":"2010","journal-title":"J. Proteom."},{"key":"2023012710385422700_btt642-B42","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S1359-6446(03)02978-7","article-title":"Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS","volume":"9","author":"Nesvizhskii","year":"2004","journal-title":"Drug Discov. Today"},{"key":"2023012710385422700_btt642-B43","doi-asserted-by":"crossref","first-page":"2779","DOI":"10.1007\/s00216-010-4142-5","article-title":"Computational mass spectrometry for metabolomics: identification of metabolites and small molecules","volume":"398","author":"Neumann","year":"2010","journal-title":"Anal. Bioanalyt. Chem."},{"key":"2023012710385422700_btt642-B44","doi-asserted-by":"crossref","first-page":"e1002296","DOI":"10.1371\/journal.pcbi.1002296","article-title":"Computational and statistical analysis of protein mass spectrometry data","volume":"8","author":"Noble","year":"2012","journal-title":"PLoS Comput Biol."},{"key":"2023012710385422700_btt642-B45","doi-asserted-by":"crossref","first-page":"2220","DOI":"10.1021\/ac035258x","article-title":"High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS\/MS de novo sequencing results","volume":"76","author":"Searle","year":"2004","journal-title":"Anal. Chem."},{"key":"2023012710385422700_btt642-B46","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1093\/bib\/bbm064","article-title":"ROC analysis: applications to the classification of biological sequences and 3D structures","volume":"9","author":"Sonego","year":"2008","journal-title":"Brief. Bioinform."},{"key":"2023012710385422700_btt642-B47","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1021\/pr070444v","article-title":"Accurate annotation of peptide modifications through unrestrictive database search","volume":"7","author":"Tanner","year":"2008","journal-title":"J. Proteome Res."},{"key":"2023012710385422700_btt642-B48","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1002\/pmic.200900433","article-title":"Data maximization by multipass analysis of protein mass spectra","volume":"10","author":"Tharakan","year":"2010","journal-title":"Proteomics"},{"key":"2023012710385422700_btt642-B49","first-page":"157","article-title":"Identification of post-translational modifications via blind search of mass-spectra","volume-title":"Proceedings\/IEEE Computational Systems Bioinformatics Conference, CSB, San Francisco, CA, USA","author":"Tsur","year":"2005"},{"key":"2023012710385422700_btt642-B50","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1093\/bib\/bbm023","article-title":"Current trends in computational inference from mass spectrometry-based proteomics","volume":"8","author":"Webb-Robertson","year":"2007","journal-title":"Brief. Bioinform."},{"key":"2023012710385422700_btt642-B51","doi-asserted-by":"crossref","first-page":"1426","DOI":"10.1021\/ac00104a020","article-title":"Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database","volume":"67","author":"Yates","year":"1995","journal-title":"Anal. Chem."},{"key":"2023012710385422700_btt642-B52","first-page":"i399","article-title":"Open MS\/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate","volume":"26","author":"Ye","year":"2010","journal-title":"Bioinformatics (Oxford, England)"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/2\/234\/48914382\/bioinformatics_30_2_234.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/2\/234\/48914382\/bioinformatics_30_2_234.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,19]],"date-time":"2024-05-19T09:48:43Z","timestamp":1716112123000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/2\/234\/222417"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11,8]]},"references-count":53,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2014,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt642","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,1,15]]},"published":{"date-parts":[[2013,11,8]]}}}