Fast computation of entropic profiles for the detection of conservation in genomes

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7986 LNBI, Issue , 2013, Pages 277-288

  Comin, Matteo ^a   Antonello, Morris ^a  

^a UNIVERSITY OF PADOVA   (Italy)

Author keywords

computational biology; information theory; pattern discovery

Indexed keywords

BIOINFORMATICS; COMPUTATION THEORY; GENES; INFORMATION THEORY;

COMPUTATIONAL BIOLOGY; FAST COMPUTATION; GENOMIC LOCATIONS; LINEAR SPACE ALGORITHMS; LINEAR TIME; PATTERN DISCOVERY;

PATTERN RECOGNITION;

EID: 84880712402     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-39159-0_25     Document Type: Conference Paper

References (26)

1. Apostolico, A., Comin, M., Parida, L.: Varun: Discovering Extensible Motifs under Saturation Constraints. IEEE/ACM Transactions on Computational Biology and Bioinformatics 7(4), 752-762 (2010)
2. Apostolico, A., Comin, M., Parida, L.: Mining, compressing and classifying with extensible motifs. Algorithms for Molecular Biology 1, 4 (2006)
3. Apostolico, A., Comin, M., Parida, L.: Bridging Lossy and Lossless Compression by Motif Pattern Discovery. In: Ahlswede, R., Bäumer, L., Cai, N., Aydinian, H., Blinovsky, V., Deppe, C., Mashurian, H. (eds.) General Theory of Information Transfer and Combinatorics. LNCS, vol. 4123, pp. 793-813. Springer, Heidelberg (2006)
4. Apostolico, A., Comin, M., Parida, L.: Motifs in Ziv-Lempel-Welch Clef. In: Proceedings of IEEE DCC Data Compression Conference, pp. 72-81. Computer Society Press (2004)
5. Bernaola-Galv́an, P., Grosse, I., Carpena, P., Oliver, J., Roḿan-Rold́an, R., Stanley, H.: Finding Borders between Coding and Noncoding DNA Regions by an Entropic Segmentation Method. Physical Review Letters 85(6), 1342-1345
6. Comin, M., Parida, L.: Subtle motif discovery for the detection of DNA regulatory sites. In: Proceeding of Asia-Pacific Bioinformatics Conference, pp. 27-36 (2007)
7. Comin, M., Parida, L.: Detection of Subtle Variations as Consensus Motifs. Theoretical Computer Science 395(2-3), 158-170 (2008)
8. Comin, M., Verzotto, D.: Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords. BMC Algorithms for Molecular Biology 7, 34 (2012)
9. Comin, M., Verzotto, D.: Whole-Genome Phylogeny by Virtue of Unic Subwords. In: Proceedings of 23rd International Workshop on Database and Expert Systems Applications, BIOKDD, pp. 190-194 (2012)
10. Comin, M., Verzotto, D.: The Irredundant Class Method for Remote Homology Detection of Protein Sequences. Journal of Computational Biology 18(12), 1819-1829 (2011)
11. Gene, Y., Burge, C.: Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals. Journal of Computional Biology 11(2-3), 377-394 (2004)
12. Hagenauer, J., Dawy, Z., Gobel, B., Hanus, P., Mueller, J.: Genomic Analysis using Methods from Information Theory. In: Information Theory Workshop, pp. 55-59 (2004)
13. Karlin, S., Mrazek, J., Campbell, A.: Frequent oligonucleotides and peptides of the Haemophilus influenzae genome. Nucleic Acids Res. 24, 4263-4272 (1996)
14. Kurtz, S., Choudhuri, J., Ohlebusch, E., Schleiermacher, C., Stoye, J., Giegerich, R.: Reputer: The manifold applications of repeat analysis on a genome scale. Nucleic Acids Res. 29(22), 4633-4642 (2001)
15. McCreight, E.M.: A space-economical suffix tree construction algorithm. Journal of ACM 23, 262-272 (1976)
16. Meek, C., Patel, J., Kasetty, S.: Oasis: An online and accurate technique for localalignment searches on biological sequences. In: Proceedings of 29th International Conference on Very Large Databases, pp. 910-921 (2003)
17. Menconi, G., Marangoni, R.: A compression-based approach for coding sequences identification. I. Application to prokaryotic genomes. J. Comput Biol. 13(8), 1477-1488 (2006)
18. Nalla, V., Rogan, P.: Automated Splicing Mutation Analysis by Information Theory. Human Mutaion 25, 334-342 (2005)
19. Schneider, T., Stormo, G., Gold, L., Ehrenfeucht, A.: Information content of binding sites on nucleotide sequences. Journal of Molecular Biology 188, 415-431 (1986)
20. Shannon, C.: A Mathematical Theory of Communication. Bell System Technical Journal 27(3), 379-423 (1948)
21. Sourice, S., Biaudet, V., El Karoui, M., Ehrlich, S.D., Gruss, A.: Identification of the Chi site of Haemophilus influenzae as several sequences related to the Escherichia coli Chi site. Mol. Microbiol. 27, 1021-1029 (1998)
22. Ukkonen, E.: On-line construction of suffix trees. Algorithmica 14(3), 249-260 (1995)
23. Vinga, S., Almeida, J.S.: Local Ŕenyi entropic profiles of DNA sequences. BMC Bioinformatics 8, 393 (2007)
24. Yockey, H.: Origin of life on earth and Shannon's theory of communication. Comput. Chem. 24(1), 105-123 (2000)
25. Waterman, M.S.: An Introduction to Computational Biology: Maps, Sequences and Genomes. Chapman Hall (1995)
26. Ziv, J., Lempel, A.: A Universal Algorithm for Sequential Data Compression. IEEE Transactions on Information Theory 23(3), 337-343 (1977)