{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,3]],"date-time":"2022-04-03T20:19:28Z","timestamp":1649017168163},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"S19","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1186\/s12859-016-1366-1","type":"journal-article","created":{"date-parts":[[2016,12,22]],"date-time":"2016-12-22T12:44:50Z","timestamp":1482410690000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms"],"prefix":"10.1186","volume":"17","author":[{"given":"Ruei-Chi","family":"Gan","sequence":"first","affiliation":[]},{"given":"Ting-Wen","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Timothy H.","family":"Wu","sequence":"additional","affiliation":[]},{"given":"Po-Jung","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Chi-Ching","family":"Lee","sequence":"additional","affiliation":[]},{"given":"Yuan-Ming","family":"Yeh","sequence":"additional","affiliation":[]},{"given":"Cheng-Hsun","family":"Chiu","sequence":"additional","affiliation":[]},{"given":"Hsien-Da","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Petrus","family":"Tang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,12,22]]},"reference":[{"issue":"1","key":"1366_CR1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","volume":"10","author":"Z Wang","year":"2009","unstructured":"Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57\u201363.","journal-title":"Nat Rev Genet"},{"issue":"7","key":"1366_CR2","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","volume":"5","author":"A Mortazavi","year":"2008","unstructured":"Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621\u20138.","journal-title":"Nat Methods"},{"issue":"1","key":"1366_CR3","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s13059-016-0881-8","volume":"17","author":"A Conesa","year":"2016","unstructured":"Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szczesniak MW, Gaffney DJ, Elo LL, Zhang X, et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016;17(1):13.","journal-title":"Genome Biol"},{"issue":"5","key":"1366_CR4","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1038\/nprot.2014.058","volume":"9","author":"TR Mercer","year":"2014","unstructured":"Mercer TR, Clark MB, Crawford J, Brunck ME, Gerhardt DJ, Taft RJ, Nielsen LK, Dinger ME, Mattick JS. Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nat Protoc. 2014;9(5):989\u20131009.","journal-title":"Nat Protoc"},{"issue":"15","key":"1366_CR5","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1093\/bioinformatics\/btp336","volume":"25","author":"R Li","year":"2009","unstructured":"Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;25(15):1966\u20137.","journal-title":"Bioinformatics"},{"issue":"9","key":"1366_CR6","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","volume":"25","author":"C Trapnell","year":"2009","unstructured":"Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105\u201311.","journal-title":"Bioinformatics"},{"issue":"5","key":"1366_CR7","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","volume":"28","author":"C Trapnell","year":"2010","unstructured":"Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511\u20135.","journal-title":"Nat Biotechnol"},{"issue":"5","key":"1366_CR8","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/nbt.1633","volume":"28","author":"M Guttman","year":"2010","unstructured":"Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol. 2010;28(5):503\u201310.","journal-title":"Nat Biotechnol"},{"issue":"11","key":"1366_CR9","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1038\/nmeth.1517","volume":"7","author":"G Robertson","year":"2010","unstructured":"Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, et al. De novo assembly and analysis of RNA-seq data. Nat Methods. 2010;7(11):909\u201312.","journal-title":"Nat Methods"},{"issue":"5","key":"1366_CR10","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"DR Zerbino","year":"2008","unstructured":"Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821\u20139.","journal-title":"Genome Res"},{"issue":"8","key":"1366_CR11","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1093\/bioinformatics\/bts094","volume":"28","author":"MH Schulz","year":"2012","unstructured":"Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012;28(8):1086\u201392.","journal-title":"Bioinformatics"},{"issue":"12","key":"1366_CR12","doi-asserted-by":"crossref","first-page":"1660","DOI":"10.1093\/bioinformatics\/btu077","volume":"30","author":"Y Xie","year":"2014","unstructured":"Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014;30(12):1660\u20136.","journal-title":"Bioinformatics"},{"issue":"7","key":"1366_CR13","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","volume":"29","author":"MG Grabherr","year":"2011","unstructured":"Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644\u201352.","journal-title":"Nat Biotechnol"},{"key":"1366_CR14","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinf. 2011;12:323.","journal-title":"BMC Bioinf"},{"issue":"1","key":"1366_CR15","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.parint.2012.09.006","volume":"62","author":"E Nagayasu","year":"2013","unstructured":"Nagayasu E, Ogura Y, Itoh T, Yoshida A, Chakraborty G, Hayashi T, Maruyama H. Transcriptomic analysis of four developmental stages of Strongyloides venezuelensis. Parasitol Int. 2013;62(1):57\u201365.","journal-title":"Parasitol Int"},{"issue":"7","key":"1366_CR16","doi-asserted-by":"crossref","first-page":"e22953","DOI":"10.1371\/journal.pone.0022953","volume":"6","author":"S Siebert","year":"2011","unstructured":"Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SH, Dunn CW. Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows. PLoS One. 2011;6(7):e22953.","journal-title":"PLoS One"},{"key":"1366_CR17","doi-asserted-by":"crossref","first-page":"619832","DOI":"10.1155\/2008\/619832","volume":"2008","author":"A Conesa","year":"2008","unstructured":"Conesa A, Gotz S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. 2008;2008:619832.","journal-title":"Int J Plant Genomics"},{"issue":"18","key":"1366_CR18","doi-asserted-by":"crossref","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","volume":"21","author":"A Conesa","year":"2005","unstructured":"Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674\u20136.","journal-title":"Bioinformatics"},{"key":"1366_CR19","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinf. 2009;10:421.","journal-title":"BMC Bioinf"},{"key":"1366_CR20","first-page":"194","volume":"120","author":"G Aparicio","year":"2006","unstructured":"Aparicio G, Gotz S, Conesa A, Segrelles D, Blanquer I, Garcia JM, Hernandez V, Robles M, Talon M. Blast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis. Stud Health Technol Inform. 2006;120:194\u2013204.","journal-title":"Stud Health Technol Inform"},{"issue":"1","key":"1366_CR21","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1093\/bioinformatics\/btr595","volume":"28","author":"Y Zhao","year":"2012","unstructured":"Zhao Y, Tang H, Ye Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics. 2012;28(1):125\u20136.","journal-title":"Bioinformatics"},{"issue":"3","key":"1366_CR22","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1101\/gr.113985.110","volume":"21","author":"SM Kielbasa","year":"2011","unstructured":"Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011;21(3):487\u201393.","journal-title":"Genome Res"},{"issue":"Web Server issu","key":"1366_CR23","doi-asserted-by":"crossref","first-page":"W348","DOI":"10.1093\/nar\/gkq448","volume":"38","author":"R Bohnert","year":"2010","unstructured":"Bohnert R, Ratsch G. rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Res. 2010;38(Web Server issue):W348\u201351.","journal-title":"Nucleic Acids Res"},{"issue":"21","key":"1366_CR24","doi-asserted-by":"crossref","first-page":"3076","DOI":"10.1093\/bioinformatics\/btr504","volume":"27","author":"W Zhao","year":"2011","unstructured":"Zhao W, Liu W, Tian D, Tang B, Wang Y, Yu C, Li R, Ling Y, Wu J, Song S, et al. wapRNA: a web-based application for the processing of RNA sequences. Bioinformatics. 2011;27(21):3076\u20137.","journal-title":"Bioinformatics"},{"issue":"5","key":"1366_CR25","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1093\/bioinformatics\/bts023","volume":"28","author":"D Hong","year":"2012","unstructured":"Hong D, Rhie A, Park SS, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, et al. FX: an RNA-Seq analysis tool on the cloud. Bioinformatics. 2012;28(5):721\u20133.","journal-title":"Bioinformatics"},{"issue":"Suppl 7","key":"1366_CR26","doi-asserted-by":"crossref","first-page":"S9","DOI":"10.1186\/1471-2164-13-S7-S9","volume":"13","author":"TW Chen","year":"2012","unstructured":"Chen TW, Gan RC, Wu TH, Huang PJ, Lee CY, Chen YY, Chen CC, Tang P. FastAnnotator-an efficient transcript annotation web tool. BMC Genomics. 2012;13 Suppl 7:S9.","journal-title":"BMC Genomics"},{"issue":"Database issue","key":"1366_CR27","first-page":"D7","volume":"42","author":"NR Coordinators","year":"2014","unstructured":"Coordinators NR. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2014;42(Database issue):D7\u201317.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"1366_CR28","first-page":"D191","volume":"42","author":"C UniProt","year":"2014","unstructured":"UniProt C. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014;42(Database issue):D191\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1366_CR29","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25\u20139.","journal-title":"Nat Genet"},{"issue":"7","key":"1366_CR30","doi-asserted-by":"crossref","first-page":"e100","DOI":"10.1093\/nar\/gkq010","volume":"38","author":"MC Frith","year":"2010","unstructured":"Frith MC, Wan R, Horton P. Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res. 2010;38(7):e100.","journal-title":"Nucleic Acids Res"},{"issue":"14","key":"1366_CR31","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754\u201360.","journal-title":"Bioinformatics"},{"key":"1366_CR32","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.ibmb.2016.01.002","volume":"70","author":"CI Keeling","year":"2016","unstructured":"Keeling CI, Li M, Sandhu HK, Henderson H, Yuen MM, Bohlmann J. Quantitative metabolome, proteome and transcriptome analysis of midgut and fat body tissues in the mountain pine beetle, Dendroctonus ponderosae Hopkins, and insights into pheromone biosynthesis. Insect Biochem Mol Biol. 2016;70:170\u201383.","journal-title":"Insect Biochem Mol Biol"},{"issue":"6","key":"1366_CR33","doi-asserted-by":"crossref","first-page":"e42","DOI":"10.1093\/nar\/gkr1248","volume":"40","author":"LY Chen","year":"2012","unstructured":"Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE. RNASEQR-a streamlined and accurate RNA-seq sequence analysis program. Nucleic Acids Res. 2012;40(6):e42.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"1366_CR34","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/S0168-9525(99)01922-8","volume":"16","author":"J Zhang","year":"2000","unstructured":"Zhang J. Protein-length distributions for the three domains of life. Trends Genet. 2000;16(3):107\u20139.","journal-title":"Trends Genet"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1366-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,28]],"date-time":"2020-09-28T05:02:08Z","timestamp":1601269328000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1366-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,12]]},"references-count":34,"journal-issue":{"issue":"S19","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["1366"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1366-1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,12]]},"article-number":"513"}}