Variable length local decoding and alignment-free sequence comparison

Theoretical Computer Science

Volumn 462, Issue , 2012, Pages 1-11

  Didier, Gilles ^a   Corel, Eduardo ^b   Laprevotte, Ivan ^c   Grossmann, Alex ^c   Landès Devauchelle, Claudine ^c  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

Author keywords

Algorithm; Coding; Genetic sequences comparison; Prefix code

Indexed keywords

ALIGNMENT-FREE SEQUENCE COMPARISON; CODING; COMPARISON OF SEQUENCES; GENETIC SEQUENCE; MEMORY SPACE; ORIGINAL ALGORITHMS; PREFIX CODES; VARIABLE LENGTH;

ALGORITHMS; ALIGNMENT;

DECODING;

EID: 84867846845     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2012.08.005     Document Type: Article

References (12)

1. V. Acuña, C-writing and classification by context (Spanish). Thesis of M.Sc. in computer science, Universidad de Chile, 2004.
2. V. Acuña, G. Didier, and A. Maass Coding with variable block maps Theoretical Computer Science 369 1-3 2006 396 405
3. G. Didier Caractérisation des n-écritures et application à l'étude des suites de complexité ultimement n+ cste Theoretical Computer Science 215 1-2 1999 31 49
4. G. Didier, L. Debomy, M. Pupin, M. Zhang, A. Grossmann, C. Devauchelle, and I. Laprevotte Comparing sequences without using alignments: application to HIV/SIV subtyping BMC Bioinformatics 8 1 2007 1
5. G. Didier, I. Laprevotte, M. Pupin, and A. Hénaut Local decoding of sequences and alignment-free comparison Journal of Computational Biology 13 8 2006 1465 1476
6. M.V. Han, and C.M. Zmasek Phyloxml: XML for evolutionary biology and comparative genomics BMC Bioinformatics 10 1 2009 356
7. D.H. Huson, and D. Bryant Application of phylogenetic networks in evolutionary studies Molecular Biology and Evolution 23 2 2006 254 267
8. C. Kuiken, K. Yusim, L. Boykin, and R. Richardson The Los Alamos Hepatitis C sequence database Bioinformatics 21 3 2005 379 384
9. J. Rissanen A universal data compression system IEEE Transactions on Information Theory 29 5 1983 656 664
10. A.R. Subramanian, M. Kaufmann, and B. Morgenstern Dialign-tx: greedy and progressive approaches for segment-based multiple sequence alignment Algorithms Molecular Biology 3 6 2008
11. J. van Helden, B. André, and J. Collado-Vides Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies 1 Journal of Molecular Biology 281 5 1998 827 842
12. S. Vinga, and J. Almeida Alignment-free sequence comparison a review Bioinformatics 19 4 2003 513 523