Supporting Online Material for “Adaptive seeds tame genomic sequence comparison”

作者: Szymon M. Kiełbasa , Martin C. Frith , Paul Horton , Kengo Sato , Raymond Wan

DOI:

关键词:

摘要: This document provides additional information to accompany the paper “Adaptive seeds tame genomic sequence comparison”. We first describe our algorithm for finding adaptive and how this is implemented in software, LAST (Section 1 – Methods). followed by results with datasets that complement expand on main 2 Additional Results). Next, we systems used experiments, more about “pooling”, dataset sources as well any default settings chosen local alignment 3 Materials). Finally, pertaining analogy Box 4 Analogy Text) some related work not mentioned given 5 Related Work).

参考文章(45)
Juha Kärkkäinen, Tommi Rantala, Engineering Radix Sort for Strings String Processing and Information Retrieval. pp. 3- 14 ,(2008) , 10.1007/978-3-540-89097-3_3
C. J. Van Rijsbergen, Karen Sparck Jones, Report on the need for and provision of an 'ideal' information retrieval test collection University of Toronto. ,(1975)
John C. Wootton, Scott Federhen, Analysis of compositionally biased regions in sequence databases. Methods in Enzymology. ,vol. 266, pp. 554- 571 ,(1996) , 10.1016/S0076-6879(96)66035-2
Stefan Burkhardt, Juha Kärkkäinen, Better filtering with gapped q-grams combinatorial pattern matching. ,vol. 56, pp. 51- 70 ,(2001) , 10.1007/3-540-48194-X_6
Simon J. Puglisi, W. F. Smyth, Andrew H. Turpin, A taxonomy of suffix array construction algorithms ACM Computing Surveys. ,vol. 39, pp. 4- ,(2007) , 10.1145/1242471.1242472
Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller, Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures PLoS Computational Biology. ,vol. 5, pp. e1000502- ,(2009) , 10.1371/JOURNAL.PCBI.1000502
K. SPARCK JONES, C.J. VAN RIJSBERGEN, INFORMATION RETRIEVAL TEST COLLECTIONS Journal of Documentation. ,vol. 32, pp. 59- 72 ,(1976) , 10.1108/EB026616
Faraz Hach, Fereydoun Hormozdiari, Can Alkan, Farhad Hormozdiari, Inanc Birol, Evan E Eichler, S Cenk Sahinalp, mrsFAST: a cache-oblivious algorithm for short-read mapping Nature Methods. ,vol. 7, pp. 576- 577 ,(2010) , 10.1038/NMETH0810-576
Martin C Frith, Michiaki Hamada, Paul Horton, Parameters for accurate genome alignment BMC Bioinformatics. ,vol. 11, pp. 80- 80 ,(2010) , 10.1186/1471-2105-11-80