EssaMEM: Finding maximal exact matches using enhanced sparse suffix arrays

Bioinformatics

Volumn 29, Issue 6, 2013, Pages 802-804

  Vyverman, Michaël ^a   De Baets, Bernard ^a   Fack, Veerle ^a   Dawyndt, Peter ^a  

^a GHENT UNIVERSITY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; COMPUTER PROGRAM; DROSOPHILA; GENETICS; GENOME; METHODOLOGY; SEQUENCE ANALYSIS;

ALGORITHMS; ANIMALS; DROSOPHILA; GENOME; SEQUENCE ANALYSIS; SOFTWARE;

EID: 84875132393     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt042     Document Type: Article

References (7)

1. Abouelhoda,M. et al. (2004) Replacing suffix trees with enhanced suffix arrays. J. Discrete Algorithms, 2, 53-86.
2. Hon,W. and Sadakane,K. (2002) Space-economical algorithms for finding maximal unique matches. In: Proceedings of the Annual Symposium on Combinatorial Pattern Matching, pp. 144-152.
3. Khan,Z. et al. (2009) A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. Bioinformatics, 25, 1609-1616.
4. Kurtz,S. et al. (2004) Versatile and open software for comparing large genomes. Genome Biol., 5, R12.
5. Navarro,G. and Makinen,V. (2007) Compressed full-text indexes. ACM Comput. Surv., 39, Article 2.
6. Ohlebusch,E. et al. (2010) Computing matching statistics and maximal exact matches on compressed full-text indexes. In: Proceedings of the 17th Annual Symposium on String Processing and Information Retrieval. Springer, pp. 347-358.
7. Vyverman,M. et al. (2012) Prospects and limitations of full-text index structures in genome analysis. Nucleic Acids Res., 40, 6993-7015.