SFA-SPA: A suffix array based short peptide assembler for metagenomic data

Bioinformatics

Volumn 31, Issue 11, 2015, Pages 1833-1835

  Yang, Youngik ^a   Zhong, Cuncong ^a   Yooseph, Shibu ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE;

ALGORITHM; CHEMISTRY; COMPUTER PROGRAM; METAGENOMICS; PROCEDURES; SEQUENCE ANALYSIS;

ALGORITHMS; METAGENOMICS; PEPTIDES; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84941641598     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv052     Document Type: Conference Paper

References (6)

1. Idury, R. M. and Waterman, M. S. (1995) A new algorithm for DNA sequence assembly. J. Comput. Biol. , 2, 291-306.
2. Kasai, T. et al. (2001) Linear-time longest-common-prefix computation in suffix arrays and its applications. In: Amir, A. (ed.) Combinatorial Pattern Matching. Springer, Berlin, pp. 181-192.
3. Manber, U. and Myers, G. (1993) Suffix arrays: A new method for on-line string searches. SIAM J. Comput. 22, 935-948.
4. Mori, Y. (2008) libdivsufsort-a lightweight suffix-sorting library. https:// code. google. com/p/libdivsufsort/. (24 February 2004, date last accessed).
5. Simon, C. and Daniel, R. (2011) Metagenomic analyses: Past and future trends. Appl. Environ. Microbiol. , 77, 1153-1161.
6. Yang, Y. and Yooseph, S. (2013) SPA: A short peptide assembler for metagenomic data. Nucleic Acids Res. , 41, e91.