References

AKO04

Mohamed Ibrahim Abouelhoda, Stefan Kurtz, and Enno Ohlebusch. Replacing suffix trees with enhanced suffix arrays. Journal of Discrete Algorithms, 2(1):53–86, 2004. doi:10.1016/S1570-8667(03)00065-0.

AC75

Alfred V Aho and Margaret J Corasick. Efficient string matching: an aid to bibliographic search. Communications of the ACM, 18(6):333–340, 1975. doi:10.1145/360825.360855.

AGM+90

Stephen F Altschul, Warren Gish, Webb Miller, Eugene W Myers, and David J Lipman. Basic local alignment search tool. Journal of molecular biology, 215(3):403–410, 1990. doi:10.1016/S0022-2836(05)80360-2.

AM97

Eric L Anson and Eugene W Myers. Realigner: a program for refining dna sequence multi-alignments. Journal of Computational Biology, 4(3):369–383, 1997. doi:10.1145/267521.267524.

BYN99

Ricardo Baeza-Yates and Gonzalo Navarro. Faster approximate string matching. Algorithmica, 23(2):127–158, 1999. doi:10.1007/PL00009253.

BCGottgens+03

Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, and Burkhard Morgenstern. Fast and sensitive multiple alignment of large genomic sequences. BMC bioinformatics, 4(1):66, 2003. doi:10.1186/1471-2105-4-66.

BDC+03

Michael Brudno, Chuong B Do, Gregory M Cooper, Michael F Kim, Eugene Davydov, Eric D Green, Arend Sidow, Serafim Batzoglou, NISC Comparative Sequencing Program, and others. Lagan and multi-lagan: efficient tools for large-scale multiple alignment of genomic dna. Genome research, 13(4):721–731, 2003. doi:10.1101/gr.926603.

Car06

Reed A Cartwright. Logarithmic gap costs decrease alignment accuracy. BMC bioinformatics, 7(1):527, 2006.

FM01

Paolo Ferragina and Giovanni Manzini. An experimental study of a compressed index. Information Sciences, 135(1):13–28, 2001. doi:10.1016/S0020-0255(01)00098-6.

GKS03

Robert Giegerich, Stefan Kurtz, and Jens Stoye. Efficient implementation of lazy suffix trees. Software: Practice and Experience, 33(11):1035–1049, 2003. doi:10.1002/spe.535.

Got82

Osamu Gotoh. An improved algorithm for matching biological sequences. Journal of molecular biology, 162(3):705–708, 1982.

Gus97

Dan Gusfield. Algorithms on strings, trees and sequences: computer science and computational biology. Cambridge University Press, 1997. ISBN 0-521-58519-8.

Hor80

R Nigel Horspool. Practical fast searching in strings. Software: Practice and Experience, 10(6):501–506, 1980. doi:10.1002/spe.4380100608.

MM93

Udi Manber and Gene Myers. Suffix arrays: a new method for on-line string searches. SIAM Journal on Computing, 22(5):935–948, 1993.

MWM+08

Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer, and Barbara Wold. Mapping and quantifying mammalian transcriptomes by rna-seq. Nature methods, 5(7):621–628, 2008. doi:10.1038/nmeth.1226.

Mye99

Gene Myers. A fast bit-vector algorithm for approximate string matching based on dynamic programming. Journal of the ACM (JACM), 46(3):395–415, 1999. doi:10.1145/316542.316550.

Pea90

William R Pearson. Rapid and sensitive sequence comparison with fastp and fasta. Methods in enzymology, 183:63–98, 1990. doi:10.1016/0076-6879(90)83007-V.

REW+08

Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cedric Notredame, and Knut Reinert. Segment-based multiple sequence alignment. Bioinformatics, 24(16):i187–i192, 2008. doi:10.1093/bioinformatics/btn281.

RKD+09

Tobias Rausch, Sergey Koren, Gennady Denisov, David Weese, Anne-Katrin Emde, Andreas Döring, and Knut Reinert. A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics, 25(9):1118–1124, 2009. doi:10.1093/bioinformatics/btp131.

THG94

Julie D Thompson, Desmond G Higgins, and Toby J Gibson. Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research, 22(22):4673–4680, 1994. doi:10.1093/nar/22.22.4673.

Ukk85

Esko Ukkonen. Finding approximate patterns in strings. Journal of algorithms, 6(1):132–137, 1985. doi:10.1016/0196-6774(85)90023-9.

UPA+14

Gianvito Urgese, Giulia Paciello, Andrea Acquaviva, Elisa Ficarra, Mariagrazia Graziano, and Maurizio Zamboni. Dynamic gap selector: a smith waterman sequence alignment algorithm with affine gap model optimisation. In In Proc. 2nd Int. Work-Conf. Bioinform. Biomed. Eng.(IWBBIO): 7-9 April 2014; Granada, 1347–1358. Copicentro Granada SL, 2014. URL: https://iwbbio.ugr.es/2014/papers/IWBBIO_2014_paper_143.pdf.

WS08

David Weese and Marcel H Schulz. Efficient string mining under constraints via the deferred frequency index. In Advances in Data Mining. Medical Applications, E-Commerce, Marketing, and Theoretical Aspects, pages 374–388. Springer, 2008. doi:10.1007/978-3-540-70720-2_29.