BIND - An algorithm for loss-less compression of nucleotide sequence data

Journal of Biosciences

Volumn 37, Issue 4, 2012, Pages 785-789

  Bose, Tungadri ^a   Mohammed, Monzoorul Haque ^a   Dutta, Anirban ^a   Mande, Sharmila S ^a  

^a TATA CONSULTANCY SERVICES   (India)

Author keywords

Block length encoding; Data compression; Delta encoding; Genome compression; Genome sequences; Unary coding

Indexed keywords

ALGORITHM; BIOTECHNOLOGY; DNA; GENOME; GENOMICS;

ARTICLE; CONTROLLED STUDY; DATA PROCESSING; GENETIC ALGORITHM; INTERMETHOD COMPARISON; NUCLEOTIDE SEQUENCE; VALIDITY;

ALGORITHMS; BASE SEQUENCE; COMPUTING METHODOLOGIES; DATA COMPRESSION; INFORMATION STORAGE AND RETRIEVAL; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84866743212     PISSN: 02505991     EISSN: 09737138     Source Type: Journal    
DOI: 10.1007/s12038-012-9230-6     Document Type: Article

References (13)

1. Behzadi B and Le Fessant F 2005 DNA compression challenge revisited; in Combinatorial pattern matching: Proceedings of CPM-2005, LNCS, Jeju Island, Korea (Springer-Verlag)
2. Cao MD, Dix TI, Allison L and Mears C 2007 A simple statistical algorithm for biological sequence compression; in Proceedings of the Data Compression Conference, DCC-2007, Snowbird, Utah
3. Chen X, Li M, Ma B and Tromp J 2002 DNACompress: fast and effective DNA sequence compression. Bioinformatics 18 1696-1698
4. Cochrane G, Karsch-Mizrachi I and Nakamura Y 2011 International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 39 D15-8
5. Grumbach S and Tahi F 1994 A new challenge for compression algorithms: genetic sequences. Inform. Process. Management 30 875-886
6. Korodi G and Tabus I 2007 Normalized maximum likelihood model of order-1 for the compression of DNA sequences; in Proceedings of the Data Compression Conference, DCC-2007, Snowbird, Utah
7. Manzini G and Rastero M 2004 A simple and fast DNA compressor. Software - Practice and Experience 34 1397-1411
8. Matsumoto T, Sadakane K and Imai H 2000 Biological sequence compression algorithms; in Genome informatics: Proceedings of the 11th Workshop, Tokyo, Japan, (eds) AK Dunker, A Konagaya, S Miyano and T Takagi. pp 43-52
9. Metzker ML 2010 Sequencing technologies - the next generation. Nat. Rev. Genet. 1 31-46
10. Pinho AJ, Neves AJR and Ferreira PJSG 2008 Inverted-repeats-aware finite-context models for DNA coding; in Proceedings of the 16th European Signal Processing Conference, EUSIPCO-2008, Lausanne, Switzerland
11. Pinho AJ, Ferreira PJSG, Neves AJR and Bastos CAC 2011 On the representability of complete genomes by multiple competing finite-context (Markov) models. PLoS ONE 6 e21588
12. Rivals E, Delahaye JP, Dauchet M and Delgrange O 1996 A guaranteed compression scheme for repetitive DNA sequences; in Proceedings of the Data Compression Conference, DCC-96, Snowbird, Utah, pp 453
13. Zhang J, Chiodini R, Badr A and Zhang G 2011 The impact of next-generation sequencing on genomics. J. Genet. Genomics 38 95-109