{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,7]],"date-time":"2024-09-07T23:28:56Z","timestamp":1725751736894},"publisher-location":"Cham","reference-count":24,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319026237"},{"type":"electronic","value":"9783319026244"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013]]},"DOI":"10.1007\/978-3-319-02624-4_16","type":"book-chapter","created":{"date-parts":[[2013,10,12]],"date-time":"2013-10-12T02:21:00Z","timestamp":1381544460000},"page":"170-180","source":"Crossref","is-referenced-by-count":1,"title":["RAIDER: Rapid Ab Initio Detection of Elementary Repeats"],"prefix":"10.1007","author":[{"given":"Nathaniel","family":"Figueroa","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaolin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiajun","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Karro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"16_CR1","unstructured":"Smit, A.F.A., Hubley, R., Green, P.: RepeatMasker Open-1.0 (1996-2010), \n                  \n                    http:\/\/www.repeatmasker.org"},{"issue":"17","key":"16_CR2","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"S. Altschul","year":"1997","unstructured":"Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research\u00a025(17), 3389 (1997)","journal-title":"Nucleic Acids Research"},{"issue":"8","key":"16_CR3","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1101\/gr.88502","volume":"12","author":"Z. Bao","year":"2002","unstructured":"Bao, Z., Eddy, S.R.: Automated de novo identification of repeat sequence families in sequenced genomes. Genome Research\u00a012(8), 1269\u20131276 (2002)","journal-title":"Genome Research"},{"issue":"6","key":"16_CR4","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1093\/bib\/bbm048","volume":"8","author":"C.M. Bergman","year":"2007","unstructured":"Bergman, C.M., Quesneville, H.: Discovering and detecting transposable elements in genome sequences. Briefings in Bioinformatics\u00a08(6), 382\u2013392 (2007)","journal-title":"Briefings in Bioinformatics"},{"issue":"suppl. 1","key":"16_CR5","doi-asserted-by":"crossref","first-page":"i152","DOI":"10.1093\/bioinformatics\/bti1003","volume":"21","author":"R.C. Edgar","year":"2005","unstructured":"Edgar, R.C., Myers, E.W.: PILER: identification and classification of genomic repeats. Bioinformatics\u00a021(suppl. 1), i152\u2013i158 (2005)","journal-title":"Bioinformatics"},{"key":"16_CR6","unstructured":"Google: sparsehash - An extremely memory-efficient hash_map implementation - Google Project Hosting, \n                  \n                    http:\/\/code.google.com\/p\/sparsehash\/"},{"issue":"1","key":"16_CR7","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1101\/gr.844103","volume":"13","author":"R.C. Hardison","year":"2003","unstructured":"Hardison, R.C.: Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution. Genome Research\u00a013(1), 13\u201326 (2003)","journal-title":"Genome Research"},{"key":"16_CR8","doi-asserted-by":"crossref","unstructured":"He, D.: Using suffix tree to discover complex repetitive patterns in DNA sequences. In: Conference Proceedings: ... of Annual International Conference of the IEEE Engineering in Medicine and Biology Society, vol.\u00a01, pp. 3474\u20133477. IEEE Engineering in Medicine and Biology Society (2006)","DOI":"10.1109\/IEMBS.2006.260445"},{"key":"16_CR9","doi-asserted-by":"crossref","unstructured":"Huo, H., Wang, X., Stojkovic, V.: An Adaptive Suffix Tree Based Algorithm for Repeats Recognition in a DNA Sequence. Bioinformatics and Bioengenierring, 181\u2013184 (2009)","DOI":"10.1109\/IJCBS.2009.65"},{"issue":"1-4","key":"16_CR10","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1159\/000084979","volume":"110","author":"J. Jurka","year":"2005","unstructured":"Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., Walichiewicz, J.: Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research\u00a0110(1-4), 462\u2013467 (2005)","journal-title":"Cytogenetic and Genome Research"},{"issue":"2","key":"16_CR11","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1093\/molbev\/msm261","volume":"25","author":"J.E. Karro","year":"2008","unstructured":"Karro, J.E., Peifer, M., Hardison, R.C., Kollmann, M., von Gr\u00fcnberg, H.H.: Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure. Molecular Biology and Evolution\u00a025(2), 362\u2013374 (2008)","journal-title":"Molecular Biology and Evolution"},{"issue":"22","key":"16_CR12","doi-asserted-by":"publisher","first-page":"4633","DOI":"10.1093\/nar\/29.22.4633","volume":"29","author":"S. Kurtz","year":"2001","unstructured":"Kurtz, S., Choudhuri, J.V., Ohlebusch, E., Schleiermacher, C., Stoye, J., Giegerich, R.: REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research\u00a029(22), 4633\u20134642 (2001)","journal-title":"Nucleic Acids Research"},{"issue":"6822","key":"16_CR13","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/35057062","volume":"409","author":"E.S. Lander","year":"2001","unstructured":"Lander, E.S., et al.: Initial sequencing and analysis of the human genome. Nature\u00a0409(6822), 860\u2013921 (2001)","journal-title":"Nature"},{"issue":"3","key":"16_CR14","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1142\/S0219720004000661","volume":"2","author":"M. Li","year":"2004","unstructured":"Li, M., Ma, B., Kisman, D., Tromp, J.: Patternhunter II: highly sensitive and fast homology search. Journal of Bioinformatics and Computational Biology\u00a02(3), 417\u2013439 (2004)","journal-title":"Journal of Bioinformatics and Computational Biology"},{"key":"16_CR15","doi-asserted-by":"crossref","unstructured":"Li, R., Ye, J., Li, S., Wang, J., Han, Y., Ye, C., Wang, J., Yang, H., Yu, J., Wong, G.K.S., Wang, J.: ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Computational Biology\u00a01(4), e43 (2005)","DOI":"10.1371\/journal.pcbi.0010043"},{"key":"16_CR16","doi-asserted-by":"crossref","unstructured":"Ma, B., Tromp, J., Li, M.: PatternHunter: faster and more sensitive homology search. Bioinformatics (2002)","DOI":"10.1093\/bioinformatics\/18.3.440"},{"issue":"9","key":"16_CR17","doi-asserted-by":"publisher","first-page":"1786","DOI":"10.1101\/gr.2395204","volume":"14","author":"P.A. Pevzner","year":"2004","unstructured":"Pevzner, P.A., Tang, H., Tesler, G.: De novo repeat classification and fragment assembly. Genome Research\u00a014(9), 1786\u20131796 (2004)","journal-title":"Genome Research"},{"issue":"suppl. 1","key":"16_CR18","doi-asserted-by":"crossref","first-page":"i351","DOI":"10.1093\/bioinformatics\/bti1018","volume":"21","author":"A.L. Price","year":"2005","unstructured":"Price, A.L., Jones, N.C., Pevzner, P.A.: De novo identification of repeat families in large genomes. Bioinformatics\u00a021(suppl. 1), i351\u20138 (2005)","journal-title":"Bioinformatics"},{"issue":"1","key":"16_CR19","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/s12042-007-9007-5","volume":"1","author":"S. Saha","year":"2008","unstructured":"Saha, S., Bridges, S., Magbanua, Z.V., Peterson, D.G.: Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences. Tropical Plant Biology\u00a01(1), 85\u201396 (2008)","journal-title":"Tropical Plant Biology"},{"issue":"7","key":"16_CR20","doi-asserted-by":"publisher","first-page":"2284","DOI":"10.1093\/nar\/gkn064","volume":"36","author":"S. Saha","year":"2008","unstructured":"Saha, S., Bridges, S., Magbanua, Z.V., Peterson, D.G.: Empirical comparison of ab initio repeat finding programs. Nucleic Acids Research\u00a036(7), 2284\u20132294 (2008)","journal-title":"Nucleic Acids Research"},{"key":"16_CR21","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/1471-2229-7-38","volume":"7","author":"G. Zabala","year":"2007","unstructured":"Zabala, G., Vodkin, L.: Novel exon combinations generated by alternative splicing of gene fragments mobilized by a CACTA transposon in Glycine max. BMC Plant Biology\u00a07, 38 (2007)","journal-title":"BMC Plant Biology"},{"issue":"5","key":"16_CR22","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"D.R. Zerbino","year":"2008","unstructured":"Zerbino, D.R., Birney, E.: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research\u00a018(5), 821\u2013829 (2008)","journal-title":"Genome Research"},{"key":"16_CR23","unstructured":"Zheng, J., Lonardi, S.: Discovery of repetitive patterns in DNA with accurate boundaries \u2026 (2005)"},{"key":"16_CR24","doi-asserted-by":"crossref","unstructured":"Zhi, D., Raphael, B.J., Price, A.L., Tang, H., Pevzner, P.A.: Identifying repeat domains in large genomes. Genome Biology\u00a07(1), R7 (2006)","DOI":"10.1186\/gb-2006-7-1-r7"}],"container-title":["Lecture Notes in Computer Science","Advances in Bioinformatics and Computational Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-02624-4_16","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,23]],"date-time":"2019-05-23T06:38:13Z","timestamp":1558593493000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-02624-4_16"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013]]},"ISBN":["9783319026237","9783319026244"],"references-count":24,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-02624-4_16","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2013]]}}}