{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T10:21:49Z","timestamp":1757586109925},"publisher-location":"Berlin, Heidelberg","reference-count":19,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540258667"},{"type":"electronic","value":"9783540319504"}],"license":[{"start":{"date-parts":[[2005,1,1]],"date-time":"2005-01-01T00:00:00Z","timestamp":1104537600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005]]},"DOI":"10.1007\/11415770_29","type":"book-chapter","created":{"date-parts":[[2010,7,12]],"date-time":"2010-07-12T23:44:50Z","timestamp":1278978290000},"page":"374-388","source":"Crossref","is-referenced-by-count":8,"title":["Using Multiple Alignments to Improve Gene Prediction"],"prefix":"10.1007","author":[{"given":"Samuel S.","family":"Gross","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael R.","family":"Brent","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"29_CR1","doi-asserted-by":"crossref","first-page":"2121","DOI":"10.1101\/gr.2596504","volume":"14","author":"The MGC Project Team","year":"2004","unstructured":"The MGC Project Team. The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC). Genome Res.\u00a014, 2121\u20132127 (2004)","journal-title":"Genome Res."},{"key":"29_CR2","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1038\/nature01262","volume":"420","author":"Waterston","year":"2002","unstructured":"Waterston, et al.: Initial sequencing and comparative analysis of the mouse genome. Nature\u00a0420, 520\u2013562 (2002)","journal-title":"Nature"},{"key":"29_CR3","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","volume":"268","author":"C. Burge","year":"1997","unstructured":"Burge, C., Karlin, S.: Prediction of complete gene structures in human genomic DNA. J. Mol. Biol.\u00a0268, 78\u201394 (1997)","journal-title":"J. Mol. Biol."},{"key":"29_CR4","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1101\/gr.424203","volume":"13","author":"M. Alexandersson","year":"2003","unstructured":"Alexandersson, M., Cawley, S., Pachter, L.: SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res.\u00a013, 496\u2013502 (2003)","journal-title":"Genome Res."},{"key":"29_CR5","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1101\/gr.871403","volume":"13","author":"G. Parra","year":"2003","unstructured":"Parra, G., Agarwal, P., Abril, J.F., Wiehe, T., Fickett, J.W., Guigo, R.: Comparative gene prediction in human and mouse. Genome Res.\u00a013, 108\u2013117 (2003)","journal-title":"Genome Res."},{"issue":"suppl. 1","key":"29_CR6","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1093\/bioinformatics\/17.suppl_1.S140","volume":"17","author":"I. Korf","year":"2001","unstructured":"Korf, I., Flicek, P., Duan, D., Brent, M.R.: Integrating genomic homology into gene structure prediction. Bioinformatics\u00a017(suppl. 1), S140\u2013S148 (2001)","journal-title":"Bioinformatics"},{"key":"29_CR7","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1101\/gr.830003","volume":"13","author":"P. Flicek","year":"2003","unstructured":"Flicek, P., Keibler, E., Hu, P., Korf, I., Brent, M.R.: Leveraging the mouse genome for gene prediction in human: From whole-genome shotgun reads to a global synteny map. Genome Res.\u00a013, 46\u201354 (2003)","journal-title":"Genome Res."},{"key":"29_CR8","doi-asserted-by":"crossref","unstructured":"Tenney, A.E., Brown, R.H., Vaske, C., Lodge, J.K., Doering, T.L., Brent, M.R.: Gene prediction and verification in a compact genome with numerous small introns. Genome Res. (2004) (in press)","DOI":"10.1101\/gr.2816704"},{"key":"29_CR9","doi-asserted-by":"crossref","unstructured":"Siepel, A.C., Haussler, D.: Computational identification of evolutionary conserved exons. In: RECOMB 2004 (2004)","DOI":"10.1145\/974614.974638"},{"key":"29_CR10","unstructured":"McAuliffe, J.D., Pachter, L., Jordan, M.I.: Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Technical Report 647, Department of Statistics, University of California, Berkeley (2003)"},{"key":"29_CR11","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1093\/bioinformatics\/19.2.219","volume":"19","author":"J.S. Pedersen","year":"2003","unstructured":"Pedersen, J.S., Hein, J.: Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics\u00a019, 219\u2013227 (2003)","journal-title":"Bioinformatics"},{"key":"29_CR12","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1093\/molbev\/msh039","volume":"21","author":"A. Siepel","year":"2004","unstructured":"Siepel, A., Haussler, D.: Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol.\u00a021, 468\u2013488 (2004)","journal-title":"Mol. Biol. Evol."},{"key":"29_CR13","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. J. Mol. Evol.\u00a017, 368\u2013376 (1981)","journal-title":"J. Mol. Evol."},{"key":"29_CR14","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1101\/gr.8.12.1233","volume":"8","author":"P. Li\u00f3","year":"1998","unstructured":"Li\u00f3, P., Goldman, N.: Models of molecular evolution and phylogeny. Genome Res.\u00a08, 1233\u20131244 (1998)","journal-title":"Genome Res."},{"key":"29_CR15","first-page":"322","volume":"3","author":"M. Bulmer","year":"1986","unstructured":"Bulmer, M.: Neighboring base effects on substitution rates in pseudogenes. Mol. Biol. Evol.\u00a03, 322\u2013329 (1986)","journal-title":"Mol. Biol. Evol."},{"key":"29_CR16","doi-asserted-by":"crossref","unstructured":"Brown, R.H., Gross, S.S., Brent, M.R.: Begin at the beginning: predicting genes with 5\u2019 UTRs (2005) (submitted)","DOI":"10.1101\/gr.3696205"},{"key":"29_CR17","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","volume":"12","author":"W.J. Kent","year":"2003","unstructured":"Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., Haussler, D.: The human genome browser at UCSC. Genome Res.\u00a012, 996\u20131006 (2003)","journal-title":"Genome Res."},{"key":"29_CR18","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1101\/gr.1933104","volume":"14","author":"M. Blanchette","year":"2004","unstructured":"Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smith, A.F.A., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., Miller, W.: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res.\u00a014, 708\u2013715 (2004)","journal-title":"Genome Res."},{"key":"29_CR19","unstructured":"SGP2 home page, \n                    \n                      http:\/\/genome.imim.es\/software\/sgp2"}],"container-title":["Lecture Notes in Computer Science","Research in Computational Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/11415770_29","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,19]],"date-time":"2019-05-19T15:57:12Z","timestamp":1558281432000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/11415770_29"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005]]},"ISBN":["9783540258667","9783540319504"],"references-count":19,"URL":"https:\/\/doi.org\/10.1007\/11415770_29","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2005]]}}}