An improved algorithm for the all-pairs suffix–prefix problem

Journal of Discrete Algorithms - Tập 37 - Trang 34-43 - 2016
William H.A. Tustumi1, Simon Gog2, Guilherme P. Telles1, Felipe A. Louza1
1Institute of Computing, University of Campinas, Campinas, SP, Brazil
2Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Germany

Tài liệu tham khảo

Baker, 2012, De novo genome assembly: what every biologist should know, Nat. Methods, 9, 333, 10.1038/nmeth.1935

El-Metwally, 2013, Next-generation sequence assembly: four stages of data processing and computational challenges, PLoS Comput. Biol., 9, 10.1371/journal.pcbi.1003345

Gonnet, 1992, 66

Gusfield, 1997

Gusfield, 1992, An efficient algorithm for the all pairs suffix–prefix problem, Inf. Process. Lett., 41, 181, 10.1016/0020-0190(92)90176-V

Manber, 1993, Suffix arrays: a new method for on-line string searches, SIAM J. Comput., 22, 935, 10.1137/0222058

Ohlebusch, 2013

Puglisi, 2007, A taxonomy of suffix array construction algorithms, ACM Comput. Surv., 39, 1, 10.1145/1242471.1242472

Rachid, 2015, A practical and scalable tool to find overlaps between sequences, BioMed Res. Int., 2015, 1, 10.1155/2015/905261

Rachid, 2014, Using the Sadakane compressed suffix tree to solve the all-pairs suffix prefix problem, BioMed Res. Int., 2014, 1, 10.1155/2014/745298

Sadakane, 2007, Compressed suffix trees with full functionality, Theory Comput. Syst., 41, 589, 10.1007/s00224-006-1198-x

Steinbiss, 2012, A new efficient data structure for storage and retrieval of multiple biosequences, IEEE/ACM Trans. Comput. Biol. Bioinform., 9, 345, 10.1109/TCBB.2011.146

Weiner, 1973, Linear pattern matching algorithms, 1