{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,31]],"date-time":"2024-05-31T18:38:31Z","timestamp":1717180711084},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2008,1,28]],"date-time":"2008-01-28T00:00:00Z","timestamp":1201478400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"DOI":"10.1186\/1471-2105-9-61","type":"journal-article","created":{"date-parts":[[2008,1,29]],"date-time":"2008-01-29T07:15:08Z","timestamp":1201590908000},"source":"Crossref","is-referenced-by-count":9,"title":["Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities"],"prefix":"10.1186","volume":"9","author":[{"given":"Usman","family":"Roshan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Satish","family":"Chikkagoudar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dennis R","family":"Livesay","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,1,28]]},"reference":[{"issue":"Spec No 1","key":"2046_CR1","doi-asserted-by":"publisher","first-page":"R17","DOI":"10.1093\/hmg\/ddl046","volume":"15","author":"JS Mattick","year":"2006","unstructured":"Mattick JS, Makunin IV: Non-coding RNA. Hum Mol Genet 2006, 15(Spec No 1):R17-R29. 10.1093\/hmg\/ddl046","journal-title":"Hum Mol Genet"},{"key":"2046_CR2","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1113\/jphysiol.2006.113191","volume":"575","author":"MF Mehler","year":"2006","unstructured":"Mehler MF, Mattick JS: Non-coding RNAs in the nervous system. J Physiol 2006, 575: 333\u2013341. 10.1113\/jphysiol.2006.113191","journal-title":"J Physiol"},{"key":"2046_CR3","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","volume":"14","author":"SR Eddy","year":"1998","unstructured":"Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14: 755\u2013763. 10.1093\/bioinformatics\/14.9.755","journal-title":"Bioinformatics"},{"issue":"3","key":"2046_CR4","doi-asserted-by":"publisher","first-page":"e56","DOI":"10.1371\/journal.pcbi.0030056","volume":"3","author":"EP Nawrocki","year":"2007","unstructured":"Nawrocki EP, Eddy SR: Query-Dependent Banding (QDB) for faster RNA similarity searches. PLoS Computational Biology 2007, 3(3):e56. Infernal version 0.72 [\n                    http:\/\/infernal.janelia.org\n                    \n                  ] 10.1371\/journal.pcbi.0030056","journal-title":"PLoS Computational Biology"},{"issue":"8","key":"2046_CR5","doi-asserted-by":"publisher","first-page":"2433","DOI":"10.1093\/nar\/gki541","volume":"33","author":"PP Gardner","year":"2005","unstructured":"Gardner PP, Wilm A, Washietl S: A benchmark of multiple sequence alignment programs based upon structural RNAs. Nucleic Acids Research 2005, 33(8):2433\u20132439. 10.1093\/nar\/gki541","journal-title":"Nucleic Acids Research"},{"key":"2046_CR6","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol 1981, 147: 195\u2013197. 10.1016\/0022-2836(81)90087-5","journal-title":"J Mol Biol"},{"key":"2046_CR7","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1101\/gr.5890907","volume":"17","author":"EK Freyhult","year":"2007","unstructured":"Freyhult EK, Bollback JP, Gardner PP: Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res 2007, 17: 117\u2013125. 10.1101\/gr.5890907","journal-title":"Genome Res"},{"key":"2046_CR8","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1016\/j.cmpb.2006.11.004","volume":"85","author":"S Iyer","year":"2007","unstructured":"Iyer S, Deutsch K, Yan X, Lin B: Batch RNAi selector: a standalone program to predict specific siRNA candidates in batches with enhanced sensitivity. Comput Methods Programs Biomed 2007, 85: 203\u2013209. 10.1016\/j.cmpb.2006.11.004","journal-title":"Comput Methods Programs Biomed"},{"key":"2046_CR9","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1186\/1471-2105-4-44","volume":"4","author":"RJ Klein","year":"2003","unstructured":"Klein RJ, Eddy SR: RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics 2003, 4: 44. 10.1186\/1471-2105-4-44","journal-title":"BMC Bioinformatics"},{"key":"2046_CR10","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.1101\/gr.1011603","volume":"13","author":"K Numata","year":"2003","unstructured":"Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming LG, Hume DA, Hayashizaki Y, Tomita M: Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res 2003, 13: 1301\u20131306. 10.1101\/gr.1011603","journal-title":"Genome Res"},{"key":"2046_CR11","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215: 403\u2013410.","journal-title":"J Mol Biol"},{"issue":"10","key":"2046_CR12","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1093\/protein\/8.10.999","volume":"8","author":"S Miyazawa","year":"1995","unstructured":"Miyazawa S: A reliable sequence alignment method based upon probabilities residue correspondences. Protein Engineering 1995, 8(10):999\u20131009. 10.1093\/protein\/8.10.999","journal-title":"Protein Engineering"},{"issue":"Suppl 2","key":"2046_CR13","doi-asserted-by":"publisher","first-page":"S153","DOI":"10.1093\/bioinformatics\/18.suppl_2.S153","volume":"18","author":"U Muckstein","year":"2002","unstructured":"Muckstein U, Hofacker IL, Stadler PF: Stochastic pairwise alignments. Bioinformatics 2002, 18(Suppl 2):S153-S160.","journal-title":"Bioinformatics"},{"issue":"22","key":"2046_CR14","doi-asserted-by":"publisher","first-page":"2715","DOI":"10.1093\/bioinformatics\/btl472","volume":"22","author":"U Roshan","year":"2006","unstructured":"Roshan U, Livesay DR: Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 2006, 22(22):2715\u20132721. 10.1093\/bioinformatics\/btl472","journal-title":"Bioinformatics"},{"key":"2046_CR15","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1101\/gr.2821705","volume":"15","author":"CB Do","year":"2005","unstructured":"Do CB, Mahabhashyam MS, Brudno M, Batzoglou S: ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res 2005, 15: 330\u2013340. 10.1101\/gr.2821705","journal-title":"Genome Res"},{"key":"2046_CR16","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","volume":"30","author":"K Katoh","year":"2002","unstructured":"Katoh K, Misawa K, Kuma K, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30: 3059\u20133066. 10.1093\/nar\/gkf436","journal-title":"Nucleic Acids Res"},{"key":"2046_CR17","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/1471-2105-5-113","volume":"5","author":"RC Edgar","year":"2004","unstructured":"Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5: 113. 10.1186\/1471-2105-5-113","journal-title":"BMC Bioinformatics"},{"key":"2046_CR18","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"RC Edgar","year":"2004","unstructured":"Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32: 1792\u20131797. 10.1093\/nar\/gkh340","journal-title":"Nucleic Acids Res"},{"key":"2046_CR19","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1002\/prot.20527","volume":"61","author":"JD Thompson","year":"2005","unstructured":"Thompson JD, Koehl P, Ripp R, Poch O: BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 2005, 61: 127\u2013136. 10.1002\/prot.20527","journal-title":"Proteins"},{"key":"2046_CR20","doi-asserted-by":"publisher","first-page":"2469","DOI":"10.1002\/pro.5560071126","volume":"7","author":"K Mizuguchi","year":"1998","unstructured":"Mizuguchi K, Deane CM, Blundell TL, Overington JP: HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci 1998, 7: 2469\u20132471.","journal-title":"Protein Sci"},{"key":"2046_CR21","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1186\/1471-2105-4-47","volume":"4","author":"GP Raghava","year":"2003","unstructured":"Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ: OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics 2003, 4: 47. 10.1186\/1471-2105-4-47","journal-title":"BMC Bioinformatics"},{"key":"2046_CR22","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22: 4673\u20134680. 10.1093\/nar\/22.22.4673","journal-title":"Nucleic Acids Res"},{"key":"2046_CR23","doi-asserted-by":"publisher","first-page":"D10","DOI":"10.1093\/nar\/gkj130","volume":"34","author":"G Cochrane","year":"2006","unstructured":"Cochrane G, Aldebert P, Althorpe N, Andersson M, Baker W, Baldwin A, Bates K, Bhattacharyya S, Browne P, van den Broek A, et al.: EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res 2006, 34: D10\u201315. 10.1093\/nar\/gkj130","journal-title":"Nucleic Acids Res"},{"key":"2046_CR24","doi-asserted-by":"publisher","first-page":"D121","DOI":"10.1093\/nar\/gki081","volume":"33","author":"S Griffiths-Jones","year":"2005","unstructured":"Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A: Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005, 33: D121\u2013124. 10.1093\/nar\/gki081","journal-title":"Nucleic Acids Res"},{"key":"2046_CR25","unstructured":"Personal communication with Alex Bateman of the RFAM database team"},{"key":"2046_CR26","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1471-2105-2-8","volume":"2","author":"E Rivas","year":"2001","unstructured":"Rivas E, Eddy SR: Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2001, 2: 8. 10.1186\/1471-2105-2-8","journal-title":"BMC Bioinformatics"},{"issue":"7","key":"2046_CR27","doi-asserted-by":"publisher","first-page":"2454","DOI":"10.1073\/pnas.0409169102","volume":"102","author":"S Washietl","year":"2005","unstructured":"Washietl S, Hofacker IL, Stadler PF: Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci USA 2005, 102(7):2454\u20139. 10.1073\/pnas.0409169102","journal-title":"Proc Natl Acad Sci USA"},{"issue":"33","key":"2046_CR28","doi-asserted-by":"publisher","first-page":"12102","DOI":"10.1073\/pnas.0404193101","volume":"101","author":"A Coventry","year":"2004","unstructured":"Coventry A, Kleitman DJ, Berger B: Multiple sequence alignments for statistical detection of RNA secondary structure. Proc Natl Acad Sci USA 2004, 101(33):12102\u20137. 10.1073\/pnas.0404193101","journal-title":"Proc Natl Acad Sci USA"},{"issue":"20","key":"2046_CR29","doi-asserted-by":"publisher","first-page":"5932","DOI":"10.1093\/nar\/gkl511","volume":"34","author":"TM Phuong","year":"2006","unstructured":"Phuong TM, Do CB, Edgar RC, Batzoglou S: Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Research 2006, 34(20):5932\u20135942. 10.1093\/nar\/gkl511","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"2046_CR30","first-page":"45","volume":"13","author":"JA Grice","year":"1997","unstructured":"Grice JA, Hughey R, Speck D: Reduced space sequence alignment. CABIOS 1997, 13(1):45\u201353.","journal-title":"CABIOS"},{"key":"2046_CR31","unstructured":"RNA-genome alignment benchmark and tools website[\n                    http:\/\/www.cs.njit.edu\/usman\/RNAgenome\n                    \n                  ]"},{"key":"2046_CR32","volume-title":"Bioinformatics: sequence and genome analysis","author":"DW Mount","year":"2006","unstructured":"Mount DW: Bioinformatics: sequence and genome analysis. 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; 2006.","edition":"2"},{"issue":"6","key":"2046_CR33","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1002\/pro.5560040613","volume":"4","author":"WR Pearson","year":"1995","unstructured":"Pearson WR: Comparison of methods for searching protein sequence databases. Protein Science 1995, 4(6):1145\u201360.","journal-title":"Protein Science"},{"key":"2046_CR34","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1186\/1471-2105-7-444","volume":"7","author":"T Hulsen","year":"2006","unstructured":"Hulsen T, de Vlieg JAM, Leunissen JMA, Groenen P: Testing statistical significance scores of sequence comparison methods with structure similarity. BMC Bioinformatics 2006, 7: 444. 10.1186\/1471-2105-7-444","journal-title":"BMC Bioinformatics"},{"key":"2046_CR35","doi-asserted-by":"crossref","DOI":"10.4135\/9781849208499","volume-title":"100 Statistical tests","author":"GK Kanji","year":"2006","unstructured":"Kanji GK: 100 Statistical tests. 3rd edition. Sage Publications; 2006.","edition":"3"},{"key":"2046_CR36","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1093\/bioinformatics\/15.1.87","volume":"15","author":"JD Thompson","year":"1999","unstructured":"Thompson JD, Plewniak F, Poch O: BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 1999, 15: 87\u201388. 10.1093\/bioinformatics\/15.1.87","journal-title":"Bioinformatics"},{"key":"2046_CR37","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/S0097-8485(96)80004-0","volume":"20","author":"M Gribskov","year":"1996","unstructured":"Gribskov M, Robinson NL: Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput Chem 1996, 20: 25\u201333. 10.1016\/S0097-8485(96)80004-0","journal-title":"Comput Chem"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-61.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-9-61\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-61.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T08:56:34Z","timestamp":1548147394000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-61"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,1,28]]},"references-count":37,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2046"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-61","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,1,28]]},"article-number":"61"}}