Conference Paper2017

Cloud-POA: A cloud-based map only implementation of PO-MSA on Amazon multi-node EC2 Hadoop Cluster

Nafis Neehal, Dewan Ziaul Karim, Ashraful Islam

2017 20th International Conference of Computer and Information Technology (ICCIT)

IEEE, pp. 1–6

CCDS Authors

References

  1. 1.Julie Thompson, Desmond G. Higgins, Toby J. Gibson. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673–4680[10.1093/nar/22.22.4673]
  2. 2.R. C. Edgar. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792–1797[10.1093/nar/gkh340]
  3. 3.Jay B. Dean, Sanjay Ghemawat. (2008). MapReduce. Communications of the ACM, 51(1), 107–113[10.1145/1327452.1327492]
  4. 4.R. Chenna. (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research, 31(13), 3497–3500[10.1093/nar/gkg500]
  5. 5.Desmond G. Higgins, Paul M. Sharp. (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene, 73(1), 237–244[10.1016/0378-1119(88)90330-7]
  6. 6.Christopher Lee, Catherine S. Grasso, Mark Sharlow. (2002). Multiple sequence alignment using partial order graphs. Bioinformatics, 18(3), 452–464[10.1093/bioinformatics/18.3.452]
  7. 7.Michael C. Schatz. (2009). CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics, 25(11), 1363–1369[10.1093/bioinformatics/btp236]
  8. 8.Pedro Romero. (2004). Bioinformatics: Sequence and Genome Analysis. Briefings in Bioinformatics, 5(4), 393–396[10.1093/bib/5.4.393-a]
  9. 9.Paulien Hogeweg, B. Hesper. (1984). The alignment of sets of sequences and the construction of phyletic trees: An integrated method. Journal of Molecular Evolution, 20(2), 175–186[10.1007/bf02257378]
  10. 10.Burkhard Morgenstern. (2004). DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Research, 32(Web Server), W33–W36[10.1093/nar/gkh373]
  11. 11.Tung Nguyen, Weisong Shi, Douglas M. Ruden. (2011). CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping. BMC Research Notes, 4(1), 171[10.1186/1756-0500-4-171]
  12. 12.Osamu Gotoh. (1996). Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments. Journal of Molecular Biology, 264(4), 823–838[10.1006/jmbi.1996.0679]
  13. 13.Makoto Hirosawa, Yasushi Totoki, Masaki Hoshida, Masato Ishikawa. (1995). Comprehensive study on iterative algorithms of multiple sequence alignment. Computer applications in the biosciences, 11(1), 13–18[10.1093/bioinformatics/11.1.13]
  14. 14.Christopher J. Lee. (2003). Generating consensus sequences from partialorder multiple sequence alignment graphs. Bioinformatics, 19(8), 999–1008[10.1093/bioinformatics/btg109]
  15. 15.Yu-Jung Chang, Chien-Chih Chen, Chuen-Liang Chen, Jan-Ming Ho. (2012). A de novo next generation genomic sequence assembler based on string graph and MapReduce cloud computing framework. BMC Genomics, 13(S7), S28[10.1186/1471-2164-13-s7-s28]
  16. 16.Serita M. Nelesen, Keechul Jung Qiaoge Liu, Donggao Zhao, C. Randal Linder, Tandy Warnow. (2007). THE EFFECT OF THE GUIDE TREE ON MULTIPLE SEQUENCE ALIGNMENTS AND SUBSEQUENT PHYLOGENETIC ANALYSES. , 25–36[10.1142/9789812776136_0004]