A meta-genome sequencing and assembly preprocessing algorithm inspired by restriction site base composition

Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012

Volumn , Issue , 2012, Pages 696-703

  Bonham Carter, Oliver ^a   Ali, Hesham ^a   Bastola, Dhundy ^a  

^a UNIVERSITY OF NEBRASKA AT OMAHA   (United States)

Author keywords

Base composition; palindromes; Restriction sites; Spectrum sets

Indexed keywords

ASSEMBLY TASKS; BASE COMPOSITION; PALINDROMES; PRE-PROCESSING ALGORITHMS; PRE-PROCESSING STEP; PROOF OF CONCEPT; RESTRICTION SITES; SPECTRUM SETS;

ALGORITHMS; BIOINFORMATICS;

BIOLOGY;

EID: 84875617781     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBMW.2012.6470222     Document Type: Conference Paper

References (19)

1. C. Venter and et al.. "The sequence of the human genome," Science, vol. 291, no. 5507, pp. 1304-1351, 2001.
2. S. DiGuistini, N. Liao, D. Platt, G. Robertson, M. Seidel, S. Chan, R. Docking, 1. Birol, R. Holt, M. Hirst, E. Mardis, M. Marra, R. Hamelin, J. Bohlmann, C. Breuil, and S. Jones, "De novo genome sequence assembly of a filamentous fungus using sanger, 454 and illumina sequence data," Genome Biology, vol. 10, no. 9, p. R94, 2009.
3. S. Schuster, "Next-generation sequencing transforms today's biology," Nature Methods, vol. 5, pp. 16-18, 2008.
4. R. Li, H. Zhu, J. Ruan, W. Qian, X. Fang, Z. Shi, Y. Li, S. Li, G. Shan, K. Kristiansen, S. Li, H. Yang, J. Wang, and J. Wang, "De novo assembly of human genomes with massively parallel short read sequencing," Genome Res, vol. 20, pp. 265-272, 2010.
5. R. Garg, R. Patel, A. Tyagi, and M. Jain, "De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification," DNA Research, vol. 18, pp. 53-63, 2011.
6. Y. Ji, Y. Shi, G. Ding, and Y. Li, "A new strategy for better genome assembly from very short reads," BMC Bioinformatics, vol. 12, no. 493, 2011.
7. D. Zerbino, G. McEwen, E. Margulies, and E. Birney, "Pebble and rock band: Heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler," PLoS One., vol. 4, no. 12, 2009.
8. W. Zhang, J. Chen, Y. Yang, Y. Tang, J. Shang, and B. Shen. "A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies," PLoS One, vol. 6, no. 3, 2011.
9. M. Hossain, N. Azimi, and S. Skiena, "Crystallizing shortread assemblies around seeds," BMC Bioinformatics, vol. 10, no. Suppl 1, 2009.
10. W.-K. W. Douglas W Bryant Jr. and T. C. Mockler, "Qsra a quality-value guided de novo short read assembler," BMC Bioinformatics, vol. 10, no. 69, 2009.
11. Q. Peng and A. Smith, "Multiple sequence assembly from reads alignable to a common reference genome." IEEE/ACM Trans Comput Bioi Bioinform., vol. 8, no. 5, 2011.
12. M. P. Lamprea-Burgunder E, Ludin P, "Species-specific typing of dna based on palindrome frequency patterns," DNA Res., vol. 18, no. 2, pp. 117-24, April 2011.
13. R. Hershberg and D. Petrov, "Evidence that mutation is universally biased towards at in bacteria," PLoS Genet, vol. 6, no. 9, 2010.
14. F. Hildebrand, A. Meyer, and A. Eyre-Walker, "Evidence of selection upon genomic gc-content in bacteria," PLoS Genet, vol. 6, no. 9, 2010.
15. J. Lightfield, N. Fram, and B. Ely, "Across bacterial phyla, distantly-related genomes with similar genomic gc content have similar patterns of amino acid usage," PLoS ONE, vol. 6, no. 3, 2011.
16. D. Richter, F. Ott, A. Auch, R. Schmid, and D. Huson, "Metasim: A sequencing simulator for genomics and metagenomics," PLoS ONE, vol. 3, no. 10, 2008.
17. M. Gelfand and E. Koonin, "Evidence of selection upon genomic gc-content in bacteria," Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes, vol. 25, no. 12, pp. 2430-2439, 1997.
18. R. Kolde, "pheatmap: Pretty heatmaps. r package version 0.6.1." http://CRAN.R-project.org/packageepheatmap, 2012.
19. R Development Core Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2012.