Space efficient computation of rare maximal exact matches between multiple sequences. Export

@article{citeulike:3644278, abstract = {In this article, we propose a new method for computing rare maximal exact matches between multiple sequences. A rare match between k sequences S(1), ... , S(k) is a string that occurs at most t(i)-times in the sequence S(i), where the t(i) > 0 are user-defined thresholds. First, the suffix tree of one of the sequences (the reference sequence) is built, and then the other sequences are matched separately against this suffix tree. Second, the resulting pairwise exact matches are combined to multiple exact matches. A clever implementation of this method yields a very fast and space efficient program. This program can be applied in several comparative genomics tasks, such as the identification of synteny blocks between whole genomes.}, author = {Ohlebusch, E. and Kurtz, S.}, citeulike-article-id = {3644278}, citeulike-linkout-0 = {http://dx.doi.org/10.1089/cmb.2007.0105}, citeulike-linkout-1 = {http://www.liebertonline.com/doi/abs/10.1089/cmb.2007.0105}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18361760}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18361760}, doi = {10.1089/cmb.2007.0105}, issn = {1066-5277}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, keywords = {algorithm, exact, matches, maximal, mems, multiple, rare, sequences}, month = {May}, number = {4}, pages = {357--377}, posted-at = {2008-11-21 11:09:28}, priority = {2}, title = {Space efficient computation of rare maximal exact matches between multiple sequences.}, url = {http://dx.doi.org/10.1089/cmb.2007.0105}, volume = {15}, year = {2008} }

TY - JOUR ID - citeulike:3644278 L3 - citeulike-article-id:3644278 N2 - In this article, we propose a new method for computing rare maximal exact matches between multiple sequences. A rare match between k sequences S(1), ... , S(k) is a string that occurs at most t(i)-times in the sequence S(i), where the t(i) > 0 are user-defined thresholds. First, the suffix tree of one of the sequences (the reference sequence) is built, and then the other sequences are matched separately against this suffix tree. Second, the resulting pairwise exact matches are combined to multiple exact matches. A clever implementation of this method yields a very fast and space efficient program. This program can be applied in several comparative genomics tasks, such as the identification of synteny blocks between whole genomes. IS - 4 JF - Journal of computational biology : a journal of computational molecular cell biology SN - 1066-5277 EP - 377 TI - Space efficient computation of rare maximal exact matches between multiple sequences. VL - 15 SP - 357 KW - algorithm KW - exact KW - matches KW - maximal KW - mems KW - multiple KW - rare KW - sequences AU - Ohlebusch, E AU - Kurtz, S PY - 2008/05// UR - http://dx.doi.org/10.1089/cmb.2007.0105 ER -