{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T15:59:25Z","timestamp":1725551965883},"publisher-location":"Berlin, Heidelberg","reference-count":27,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642124754"},{"type":"electronic","value":"9783642124761"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010]]},"DOI":"10.1007\/978-3-642-12476-1_13","type":"book-chapter","created":{"date-parts":[[2010,4,8]],"date-time":"2010-04-08T13:46:37Z","timestamp":1270734397000},"page":"182-195","source":"Crossref","is-referenced-by-count":7,"title":["Unified View of Backward Backtracking in Short Read Mapping"],"prefix":"10.1007","author":[{"given":"Veli","family":"M\u00e4kinen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niko","family":"V\u00e4lim\u00e4ki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antti","family":"Laaksonen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riku","family":"Katainen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"13_CR1","unstructured":"Burrows, M., Wheeler, D.: A block sorting lossless data compression algorithm. Technical Report 124, Digital Equipment Corporation (1994)"},{"key":"13_CR2","doi-asserted-by":"crossref","unstructured":"Cole, R., Gottlieb, L.-A., Lewenstein, M.: Dictionary matching and indexing with errors and don\u2019t cares. In: Proceedings of the Thirty Sixth Annual Symposium on the Theory of Computing, pp. 91\u2013100 (2004)","DOI":"10.1145\/1007352.1007374"},{"key":"13_CR3","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1038\/ng.406","volume":"41","author":"Tuupanen","year":"2009","unstructured":"Tuupanen, et al.: The common colorectal cancer predisposition snp rs6983267 at chromosome 8q24 confers potential to enhanced wnt signaling. Nature Genetics\u00a041, 885\u2013890 (2009)","journal-title":"Nature Genetics"},{"issue":"4","key":"13_CR4","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1145\/1082036.1082039","volume":"52","author":"P. Ferragina","year":"2005","unstructured":"Ferragina, P., Manzini, G.: Indexing compressed texts. Journal of the ACM\u00a052(4), 552\u2013581 (2005)","journal-title":"Journal of the ACM"},{"issue":"2","key":"13_CR5","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1145\/1240233.1240243","volume":"3","author":"P. Ferragina","year":"2007","unstructured":"Ferragina, P., Manzini, G., M\u00e4kinen, V., Navarro, G.: Compressed representations of sequences and full-text indexes. ACM Transactions on Algorithms (TALG)\u00a03(2), article 20 (2007)","journal-title":"ACM Transactions on Algorithms (TALG)"},{"key":"13_CR6","doi-asserted-by":"crossref","unstructured":"Gabow, H.N., Bentley, J.L., Tarjan, R.E.: Scaling and related techniques for geometry problems. In: Proc. 16th ACM Symposium on Theory of Computing (STOC 1984), pp. 135\u2013143 (1984)","DOI":"10.1145\/800057.808675"},{"key":"13_CR7","doi-asserted-by":"crossref","unstructured":"Harismendy, O., Ng, P.C., Strausberg, R.L., Wang, X., Stockwell, T.B., Beeson, K.Y., Schork, N.J., Murray, S.S., Topol, E.J., Levy, S., Frazer, K.A.: Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biology\u00a010(R10) (2009)","DOI":"10.1186\/gb-2009-10-3-r32"},{"issue":"5830","key":"13_CR8","doi-asserted-by":"publisher","first-page":"1497","DOI":"10.1126\/science.1141319","volume":"316","author":"D.S. Johnson","year":"2007","unstructured":"Johnson, D.S., Mortazavi, A., Myers, R.M., Wold, B.: Genome-wide mapping of in vivo protein-dna interactions. Science\u00a0316(5830), 1497\u20131502 (2007)","journal-title":"Science"},{"issue":"16","key":"13_CR9","doi-asserted-by":"publisher","first-page":"5221","DOI":"10.1093\/nar\/gkn488","volume":"36","author":"R. Jothi","year":"2008","unstructured":"Jothi, R., Cuddapah, S., Barski, A., Cui, K., Zhao, K.: Genome-wide identification of in vivo protein-dna binding sites from chip-seq data. Nucl. Acids Res.\u00a036(16), 5221\u20135231 (2008)","journal-title":"Nucl. Acids Res."},{"key":"13_CR10","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1137\/1.9781611972870.8","volume-title":"Proc. 9th Workshop on Algorithm Engineering and Experiments (ALENEX 2007)","author":"J. K\u00e4rkk\u00e4inen","year":"2007","unstructured":"K\u00e4rkk\u00e4inen, J., Na, J.C.: Faster filters for approximate string matching. In: Proc. 9th Workshop on Algorithm Engineering and Experiments (ALENEX 2007), pp. 84\u201390. SIAM, Philadelphia (2007)"},{"issue":"6","key":"13_CR11","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1093\/bioinformatics\/btn032","volume":"24","author":"T.W. Lam","year":"2008","unstructured":"Lam, T.W., Sung, W.K., Tam, S.L., Wong, C.K., Yiu, S.M.: Compressed indexing and local alignment of dna. Bioinformatics\u00a024(6), 791\u2013797 (2008)","journal-title":"Bioinformatics"},{"issue":"3","key":"13_CR12","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B. Langmead","year":"2009","unstructured":"Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L.: Ultrafast and memory-efficient alignment of short dna sequences to the human genome. Genome Biology\u00a010(3), R25 (2009)","journal-title":"Genome Biology"},{"key":"13_CR13","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1101\/gr.078212.108","volume":"18","author":"H. Li","year":"2008","unstructured":"Li, H., Ruan, J., Durbin, R.: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research\u00a018, 1851\u20131858 (2008)","journal-title":"Genome Research"},{"key":"13_CR14","doi-asserted-by":"crossref","unstructured":"Li, H., Durbin, R.: Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics (2009) (Advance access)","DOI":"10.1093\/bioinformatics\/btp324"},{"issue":"5","key":"13_CR15","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1093\/bioinformatics\/btn025","volume":"24","author":"R. Li","year":"2008","unstructured":"Li, R., Li, Y., Kristiansen, K., Wang, J.: Soap: short oligonucleotide alignment program. Bioinformatics\u00a024(5), 713\u2013714 (2008)","journal-title":"Bioinformatics"},{"issue":"15","key":"13_CR16","doi-asserted-by":"publisher","first-page":"1966","DOI":"10.1093\/bioinformatics\/btp336","volume":"25","author":"R. Li","year":"2009","unstructured":"Li, R., Yu, C., Li, Y., Lam, T.-W., Yiu, S.-M., Kristiansen, K., Wang, J.: Soap2. Bioinformatics\u00a025(15), 1966\u20131967 (2009)","journal-title":"Bioinformatics"},{"key":"13_CR17","doi-asserted-by":"crossref","unstructured":"M\u00e4kinen, V.: Parameterized Approximate String Matching and Local-Similarity-Based Point-Pattern Matching. PhD thesis, University of Helsinki (2003)","DOI":"10.1007\/3-540-45452-7_11"},{"key":"13_CR18","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1007\/978-3-642-02008-7_9","volume-title":"Research in Computational Molecular Biology","author":"V. M\u00e4kinen","year":"2009","unstructured":"M\u00e4kinen, V., Navarro, G., Sir\u00e9n, J., V\u00e4lim\u00e4ki, N.: Storage and retrieval of individual genomes. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol.\u00a05541, pp. 121\u2013137. Springer, Heidelberg (2009)"},{"issue":"5","key":"13_CR19","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1137\/0222058","volume":"22","author":"U. Manber","year":"1993","unstructured":"Manber, U., Myers, G.: Suffix arrays: a new method for on-line string searches. SIAM Journal on Computing\u00a022(5), 935\u2013948 (1993)","journal-title":"SIAM Journal on Computing"},{"issue":"2","key":"13_CR20","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1145\/321941.321946","volume":"23","author":"E. McCreight","year":"1976","unstructured":"McCreight, E.: A space-economical suffix tree construction algorithm. Journal of the ACM\u00a023(2), 262\u2013272 (1976)","journal-title":"Journal of the ACM"},{"key":"13_CR21","doi-asserted-by":"publisher","first-page":"81","DOI":"10.2144\/000112900","volume":"45","author":"R.D. Morin","year":"2008","unstructured":"Morin, R.D., Bainbridge, M., Fejes, A., Hirst, M., Krzywinski, M., Pugh, T.J., McDonald, H., Varhol, R., Jones, S.J.M., Marra, M.A.: Profiling the hela s3 transcriptome using randomly primed cdna and massively parallel short-read sequencing. BioTechniques\u00a045, 81\u201394 (2008)","journal-title":"BioTechniques"},{"key":"13_CR22","doi-asserted-by":"crossref","unstructured":"Navarro, G., M\u00e4kinen, V.: Compressed full-text indexes. ACM Computing Surveys\u00a039(1), article 2 (2007)","DOI":"10.1145\/1216370.1216372"},{"issue":"1","key":"13_CR23","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1145\/375360.375365","volume":"33","author":"G. Navarro","year":"2001","unstructured":"Navarro, G.: A guided tour to approximate string matching. ACM Comput. Surveys\u00a033(1), 31\u201388 (2001)","journal-title":"ACM Comput. Surveys"},{"issue":"9","key":"13_CR24","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","volume":"25","author":"C. Trapnell","year":"2009","unstructured":"Trapnell, C., Pachter, L., Salzberg, S.L.: Tophat: discovering splice junctions with Rna-seq. Bioinformatics\u00a025(9), 1105\u20131111 (2009)","journal-title":"Bioinformatics"},{"issue":"3","key":"13_CR25","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1007\/BF01206331","volume":"14","author":"E. Ukkonen","year":"1995","unstructured":"Ukkonen, E.: On-line construction of suffix trees. Algorithmica\u00a014(3), 249\u2013260 (1995)","journal-title":"Algorithmica"},{"issue":"1","key":"13_CR26","doi-asserted-by":"publisher","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. Nature Reviews Genetics\u00a010(1), 57\u201363 (2009)","journal-title":"Nature Reviews Genetics"},{"key":"13_CR27","doi-asserted-by":"crossref","unstructured":"Weiner, P.: Linear pattern matching algorithm. In: Proc. 14th Annual IEEE Symposium on Switching and Automata Theory, pp. 1\u201311 (1973)","DOI":"10.1109\/SWAT.1973.13"}],"container-title":["Lecture Notes in Computer Science","Algorithms and Applications"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-12476-1_13.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,24]],"date-time":"2020-11-24T02:54:26Z","timestamp":1606186466000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-12476-1_13"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010]]},"ISBN":["9783642124754","9783642124761"],"references-count":27,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-12476-1_13","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2010]]}}}