{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T23:48:17Z","timestamp":1747180097224},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2008,4,11]],"date-time":"2008-04-11T00:00:00Z","timestamp":1207872000000},"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\/1471-2105-9-190","type":"journal-article","created":{"date-parts":[[2008,4,11]],"date-time":"2008-04-11T18:14:33Z","timestamp":1207937673000},"source":"Crossref","is-referenced-by-count":5,"title":["Local conservation scores without a priori assumptions on neutral substitution rates"],"prefix":"10.1186","volume":"9","author":[{"given":"Janis","family":"Dingel","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pavol","family":"Hanus","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niccol\u00f2","family":"Leonardi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joachim","family":"Hagenauer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00fcrgen","family":"Zech","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jakob C","family":"Mueller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,4,11]]},"reference":[{"key":"2175_CR1","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1038\/nrg1527","volume":"6","author":"E Dermitzakis","year":"2005","unstructured":"Dermitzakis E, Reymond A, Antonarakis S: Conserved non-genic sequences \u2013 an unexpected feature of mammalian genomes. Nat Rev Genet 2005, 6: 151\u2013157. 10.1038\/nrg1527","journal-title":"Nat Rev Genet"},{"issue":"8","key":"2175_CR2","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1101\/gr.3715005","volume":"15","author":"A Siepel","year":"2005","unstructured":"Siepel A, Bejerano G, Pedersen JS: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15(8):1034\u20131050. 10.1101\/gr.3715005","journal-title":"Genome Res"},{"issue":"5675","key":"2175_CR3","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.1126\/science.1098119","volume":"304","author":"G Bejerano","year":"2004","unstructured":"Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D: Ultraconserved elements in the human genome. Science 2004, 304(5675):1321\u20135. 10.1126\/science.1098119","journal-title":"Science"},{"key":"2175_CR4","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1186\/1471-2105-8-417","volume":"8","author":"A Wang","year":"2007","unstructured":"Wang A, Ruzzo W, Tompa M: How accurately is ncRNA aligned within whole-genome multiple alignments? BMC Bioinformatics 2007, 8: 417. 10.1186\/1471-2105-8-417","journal-title":"BMC Bioinformatics"},{"issue":"19","key":"2175_CR5","doi-asserted-by":"publisher","first-page":"3899","DOI":"10.1093\/nar\/27.19.3899","volume":"27","author":"N Stojanovic","year":"1999","unstructured":"Stojanovic N, Florea L, Riemer C, Gumucio D, Slightom J, Goodman M, Miller W, Hardison R: Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucl Acids Res 1999, 27(19):3899\u20133910. 10.1093\/nar\/27.19.3899","journal-title":"Nucl Acids Res"},{"key":"2175_CR6","first-page":"37","volume":"8","author":"M Blanchette","year":"2000","unstructured":"Blanchette M, Schwikowski B, Tompa M: An exact algorithm to identify motifs in orthologous sequences from multiple species. Proc Int Conf Intell Syst Mol Biol 2000, 8: 37\u201345.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"2175_CR7","doi-asserted-by":"publisher","first-page":"2507","DOI":"10.1101\/gr.1602203","volume":"13","author":"E Margulies","year":"2003","unstructured":"Margulies E, Blanchette M, Haussler D, Green E: Identification and characterization of multi-species conserved sequences. Genome Res 2003, 13: 2507\u20132518. 10.1101\/gr.1602203","journal-title":"Genome Res"},{"key":"2175_CR8","first-page":"325","volume-title":"Phylogenetic Hidden Markov Models","author":"A Siepel","year":"2005","unstructured":"Siepel A, Haussler D: Phylogenetic Hidden Markov Models. Springer. Statistics for Biology and Health; 2005:325\u2013351."},{"issue":"7","key":"2175_CR9","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1101\/gr.3577405","volume":"15","author":"GM Cooper","year":"2005","unstructured":"Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A: Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 2005, 15(7):901\u201313. 10.1101\/gr.3577405","journal-title":"Genome Res"},{"issue":"12","key":"2175_CR10","doi-asserted-by":"publisher","first-page":"e254","DOI":"10.1371\/journal.pcbi.0030254","volume":"3","author":"S Asthana","year":"2007","unstructured":"Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S: Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol 2007, 3(12):e254. 10.1371\/journal.pcbi.0030254","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"2175_CR11","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1101\/gr.2034704","volume":"14","author":"GM Cooper","year":"2004","unstructured":"Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A: Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Res 2004, 14(4):539\u201348. 10.1101\/gr.2034704","journal-title":"Genome Res"},{"key":"2175_CR12","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1101\/gr.844103","volume":"13","author":"RC Hardison","year":"2003","unstructured":"Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D: Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res 2003, 13: 13\u201326. 10.1101\/gr.844103","journal-title":"Genome Res"},{"issue":"14","key":"2175_CR13","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/nature05874","volume":"447","author":"The ENCODE Project Consortium","year":"2007","unstructured":"The ENCODE Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447(14):799\u2013816. 10.1038\/nature05874","journal-title":"Nature"},{"issue":"6","key":"2175_CR14","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1101\/gr.6034307","volume":"17","author":"EH Margulies","year":"2007","unstructured":"Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, L\u00f6ytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VVB, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 2007, 17(6):760\u201374. 10.1101\/gr.6034307","journal-title":"Genome Res"},{"issue":"9","key":"2175_CR15","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.1101\/gr.6406307","volume":"17","author":"M Pheasant","year":"2007","unstructured":"Pheasant M, Mattick JS: Raising the estimate of functional human sequences. Genome Res 2007, 17(9):1245\u201353. 10.1101\/gr.6406307","journal-title":"Genome Res"},{"issue":"8","key":"2175_CR16","doi-asserted-by":"publisher","first-page":"2740","DOI":"10.1073\/pnas.0511238103","volume":"103","author":"M Kamal","year":"2006","unstructured":"Kamal M, Xie X, Lander ES: A large family of ancient repeat elements in the human genome is under strong selection. Proc Natl Acad Sci USA 2006, 103(8):2740\u20135. 10.1073\/pnas.0511238103","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"2175_CR17","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1007\/BF00160154","volume":"39","author":"Z Yang","year":"1994","unstructured":"Yang Z: Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 1994, 39(3):306\u201314. 10.1007\/BF00160154","journal-title":"J Mol Evol"},{"key":"2175_CR18","doi-asserted-by":"publisher","first-page":"552","DOI":"10.2307\/2532943","volume":"51","author":"Z Yang","year":"1995","unstructured":"Yang Z, Wang T: Mixed Model Analysis of DNA Sequence Evolution. Biometrics 1995, 51: 552\u2013561. 10.2307\/2532943","journal-title":"Biometrics"},{"issue":"2","key":"2175_CR19","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1093\/genetics\/139.2.993","volume":"139","author":"Z Yang","year":"1995","unstructured":"Yang Z: A space-time process model for the evolution of DNA sequences. Genetics 1995, 139(2):993\u20131005.","journal-title":"Genetics"},{"issue":"2","key":"2175_CR20","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1093\/sysbio\/46.2.346","volume":"46","author":"R Nielsen","year":"1997","unstructured":"Nielsen R: Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. Syst Biol 1997, 46(2):346\u201353. 10.2307\/2413628","journal-title":"Syst Biol"},{"key":"2175_CR21","doi-asserted-by":"publisher","DOI":"10.1093\/acprof:oso\/9780198567028.001.0001","volume-title":"Computational Molecular Evolution","author":"Z Yang","year":"2006","unstructured":"Yang Z: Computational Molecular Evolution. Oxford Series in Ecology and Evolution, Oxford University Press; 2006."},{"key":"2175_CR22","doi-asserted-by":"publisher","DOI":"10.1007\/0-387-27733-1","volume-title":"Statistical Methods in Molecular Evolution","author":"R Nielsen","year":"2005","unstructured":"Nielsen R: Statistical Methods in Molecular Evolution. Statistics for Biology and Health, Springer; 2005."},{"issue":"5","key":"2175_CR23","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1016\/S0168-9525(01)02272-7","volume":"17","author":"S Whelan","year":"2001","unstructured":"Whelan S, Li\u00f2 P, Goldman N: Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet 2001, 17(5):262\u201372. 10.1016\/S0168-9525(01)02272-7","journal-title":"Trends Genet"},{"key":"2175_CR24","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1093\/oxfordjournals.molbev.a025575","volume":"13","author":"J Felsenstein","year":"1996","unstructured":"Felsenstein J, Churchill GA: A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol 1996, 13: 93\u2013104.","journal-title":"Mol Biol Evol"},{"key":"2175_CR25","first-page":"171","volume-title":"fourth Recomb satellite conference on Comparative Genomics","author":"A Diallo","year":"2006","unstructured":"Diallo A, Makarenkov V, Blanchette M: Finding maximum likelihood indel scenarios. fourth Recomb satellite conference on Comparative Genomics 2006, 171\u2013185."},{"issue":"3","key":"2175_CR26","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1093\/bioinformatics\/btl578","volume":"23","author":"J Kim","year":"2007","unstructured":"Kim J, Sinha S: Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics 2007, 23(3):289\u201397. 10.1093\/bioinformatics\/btl578","journal-title":"Bioinformatics"},{"issue":"6","key":"2175_CR27","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1007\/BF01734359","volume":"17","author":"J Felsenstein","year":"1981","unstructured":"Felsenstein J: Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981, 17(6):368\u201376. 10.1007\/BF01734359","journal-title":"J Mol Evol"},{"issue":"9","key":"2175_CR28","first-page":"367","volume":"11","author":"Z Yang","year":"1996","unstructured":"Yang Z: Among-site rate variation and its impact on phylogenetic analyses. TREE 1996, 11(9):367\u2013372.","journal-title":"TREE"},{"issue":"3","key":"2175_CR29","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1093\/biomet\/56.3.627","volume":"56","author":"PAP Moran","year":"1969","unstructured":"Moran PAP: Statistical inference with bivariate gamma distributions. Biometrika 1969, 56(3):627\u2013634. 10.1093\/biomet\/56.3.627","journal-title":"Biometrika"},{"key":"2175_CR30","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1007\/BF01543811","volume":"1","author":"RM Phatarfod","year":"1987","unstructured":"Phatarfod RM: A linearly regressive Gamma Markov process. Stochastic Hydrology ans Hydraulics 1987, 1: 155\u2013160. 10.1007\/BF01543811","journal-title":"Stochastic Hydrology ans Hydraulics"},{"key":"2175_CR31","first-page":"190","volume-title":"Lect Notes Comput Sci","author":"A Siepel","year":"2006","unstructured":"Siepel A, Pollard KS, Haussler D: New methods for detecting lineage-specific selection. In Lect Notes Comput Sci. Volume 3909. Edited by: Davis, CA. LNBI of 10th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2006, U.C. Davis Genome Center, Dept. of Stats; 2006:190\u2013205. 10.1007\/11732990_17"},{"key":"2175_CR32","volume-title":"Genome Res","author":"DM McGaughey","year":"2007","unstructured":"McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, McCallion AS: Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res 2007."},{"issue":"14","key":"2175_CR33","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1038\/447760a","volume":"447","author":"E Check","year":"2007","unstructured":"Check E: Genome Project turns up evolutionary surprises. Nature 2007, 447(14):760\u2013761. 10.1038\/447760a","journal-title":"Nature"},{"issue":"4","key":"2175_CR34","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1101\/gr.1933104","volume":"14","author":"M Blanchette","year":"2004","unstructured":"Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004, 14(4):708\u201315. 10.1101\/gr.1933104","journal-title":"Genome Res"},{"key":"2175_CR35","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1093\/nar\/gkg129","volume":"31","author":"D Karolchik","year":"2003","unstructured":"Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, WJK : The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31: 51\u20134. 10.1093\/nar\/gkg129","journal-title":"Nucleic Acids Res"},{"key":"2175_CR36","doi-asserted-by":"publisher","DOI":"10.1002\/0471200611","volume-title":"Elements of Information Theory","author":"TM Cover","year":"1991","unstructured":"Cover TM, Thomas JA: Elements of Information Theory. Wiley Series In Telecommunications, Wiley-Interscience; 1991."},{"issue":"2","key":"2175_CR37","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1109\/18.485714","volume":"42","author":"J Hagenauer","year":"1996","unstructured":"Hagenauer J, Offer E, Papke L: Iterative decoding of binary block and convolutional codes. IEEE Transactions on Information Theory 1996, 42(2):429\u2013445. 10.1109\/18.485714","journal-title":"IEEE Transactions on Information Theory"},{"key":"2175_CR38","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/1471-2105-6-63","volume":"6","author":"E Rivas","year":"2005","unstructured":"Rivas E: Evolutionary models for insertions and deletions in a probabilistic modeling framework. BMC Bioinformatics 2005, 6: 63. 10.1186\/1471-2105-6-63","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-190.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-9-190\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-190.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,7]],"date-time":"2021-09-07T21:42:44Z","timestamp":1631050964000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-190"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,4,11]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2175"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-190","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,4,11]]},"article-number":"190"}}