Short read DNA fragment anchoring algorithm

BMC Bioinformatics

Volumn 10, Issue SUPPL. 1, 2009, Pages

  Wang, Wendi ^a   Zhang, Peiheng ^a   Liu, Xinchun ^a  

^a INSTITUTE OF COMPUTING TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM EFFICIENCY; COMPUTATIONAL BOTTLENECKS; DNA FRAGMENT; GENE FRAGMENTS; GENOME SEQUENCING; NEXT-GENERATION SEQUENCING; OUTPUT SEQUENCES; PCR TECHNOLOGY;

ALGORITHMS; BIOINFORMATICS; GENES; POLYMERASE CHAIN REACTION; EFFICIENCY;

EFFICIENCY; BIOINFORMATICS;

DNA;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; DNA SEQUENCE; GENETIC DATABASE; GENETICS; HUMAN; HUMAN GENOME; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT;

ALGORITHMS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA; GENOME, HUMAN; HUMANS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 60849114000     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S1-S17     Document Type: Article

References (32)

1. Genome Analyzer System http://www.illumina.com/
2. Weber L James Myers W Eugene Human Whole-Genome Shotgun Sequencing Genome Res 1997, 7:401-409 9149936
3. Ning Z Cox AJ Mullikin JC SSAHA: A fast search method for large DNA databases Genome Res 2001, 11:1725-1729 311141 11591649
4. Chaisson MJ Pevzner PA Short read fragment assembly of bacterial genomes Genome Res 18, 2:324-330 February 1, 2008
5. Ruiqiang Li et al. SOAP: Short oligonucleotide alignment program Bioinformatics 2008, 24:713-714 18227114
6. Francisco M Marth T Gabor Granger S Computational tools for next-generation sequencing applications Pacific Symposium on Biocomputing 13, 87-89
7. Smith TF Waterman MS Identification of Common Molecular Subsequences Journal of Molecular Biology 1981, 147(1):195-197 7265238
8. Navarro G A guided tour to approximate string matching ACM Computing Surveys 2001, 33(1):31-88
9. Pearson WR Lipman DJ Improved tools for biological sequence comparison Proc Natl Acad Sci 1988, 85:2444-2448 280013 3162770
10. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215:403-410 2231712
11. Gibbs AJ McIntyre GA The diagram, a method for comparing sequences. It's use with amino acid and nucleotide sequences Eur J Biochem 1970, 16:1-11 5456129
12. Cooper G Raymer M Doom T Krane D Futamur N Indexing genomic databases Fourth IEEE symposium on bioinformatics and bioengineering (BIBE'04), Taichung, Taiwan 2004
13. Kahveci T Singh AK An Efficient Index Structure for String Databases VLDB, Roma, Italy 2001, 351-360
14. Myers E An O(ND) difference algorithm and its variations Algorithmica 1986, 251-266
15. Ferhatosmanoglu H Tuncel E Agrawal D El Abbadi A Vector Approximation based Indexing for Non-uniform High Dimensional Data Sets Proceedings of the 9th ACM International Conference on Information and Knowledge Management (CIKM), Washington, DC, USA 2000, 202-209
16. Califano A Rigoutsos I FLASH: A fast look-up algorithm for string homology International conference on intelligent systems for molecular biology, Bethesda, MD 1993, 56-64
17. Michailidis PD Margaritis KG A programmable array processor architecture for flexible approximate string matching algorithms J Parallel Distrib Comput 2007, 67:131-141
18. Kent WJ BLAT: The BLAST-like alignment tool Genome Research 2002, 12:656-664 187518 11932250
19. Lee HP Tsai YT Sheu TF Tang CT An IDC-based algorithm for efficient homology filtration with guaranteed seriate coverage Fourth IEEE symposium on bioinformatics and bioengineering (BIBE'04), Taichung, Taiwan 2004
20. Sun Hong Ozturk Ozgur Ferhatosmanoglu Hakan CoMRI: A Compressed Multi-Resolution Index Structure for Sequence Similarity Queries IEEE Computer Society Bioinformatics Conference (CSB'03) 2003, 553
21. Ozturk O Ferhatosmanoglu H Effective Indexing and Filtering for Similarity Search in Large Biosequence Databases Proc of IEEE Sym on Bioinformatics and Bioengineering 2003, 359-366
22. Oliver T Yeow LY Schmidt B High Performance Database Searching with HMMer on FPGAs IPDPS 2007 200,7 1-7
23. Buhler Jeremy Keich Uri Sun Yanni Designing seeds for similarity search in genomic DNA Journal of Computer and System Sciences 2005, 70:342-363
24. Makinen Veli Navarro Gonzalo Succinct suffix arrays based on run-length encoding Nordic Journal of Computing 2005
25. Ming L Bin M Derek K John T PatternHuter II: Highly Sensitive and Fast Homology Search Genome Informatics 2003, 14:164-175 15706531
26. Bergroth L Hakonen H Raita T A survey of longest common subsequence algorithms Proceedings of the 7th International Symposium on String Processing and Information Retrieval 2000, 39-48
27. Henikoff S Henikoff JG Amino acid substitution matrices from protein blocks Proc Natl Acad Sci 1992, 89:10915-10919 50453 1438297
28. Mount DW Bioinformatics Sequence and Genome Analysis Cold Spring Harbor Laboratory Press 2001
29. Dohm JC Lottaz C Borodina T Himmelbauer H SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing Genome Res 2007, 17(11):1697-1706 2045152 17908823
30. Maq http://maq.sourceforge.net/index.shtml
31. Human Genome Resources http://www.ncbi.nlm.nih.gov
32. Karlin S Altschul SF Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes Proc Natl Acad Sci 87, 2264-2268