Multiple genome alignment by clustering pairwise matches

Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science)

Volumn 3388, Issue , 2005, Pages 30-41

  Choi, Jeong Hyeon ^a,b   Choi, Kwangmin ^a   Cho, Hwan Gue ^b   Kim, Sun ^a  

^a INDIANA UNIVERSITY   (United States)

^b Pusan National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; MOLECULAR BIOLOGY; PERFORMANCE; PROBLEM SOLVING; ALIGNMENT; GENES; MICROBIOLOGY;

MULTIPLE GENOME ALIGNMENT; SEQUENCE CLUSTERING ALGORITHMS;

GENES; GENETIC ENGINEERING;

GENOME ALIGNMENT; MULTIPIPMAKER (MPM); SEQUENCE CLUSTERING ALGORITHM;

EID: 26444589766     PISSN: 03029743     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1007/978-3-540-32290-0_3     Document Type: Conference Paper

References (20)

1. Kellis, M., Patterson, N., Endrizzi, M., Birren, B., Lander, E.: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423 (2003) 241-254
2. Pevzner, P., Tesler, G.: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 7672-7677
3. Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., Miller, W.: Human-mouse alignments with BLASTZ. Genome Res. 13 (2003) 103-107
4. Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (1970) 443-453
5. Smith, T.F., Waterman, M.S.: Identification of common molecular sequences. J. Mol. Biol. 147 (1981) 195-197
6. Lipman, D.J., Altschul, S.F., Kececioglu, J.D.: A tool for multiple sequence alignment. Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 4412-4415
7. Thompson, J., Higgins, D., Gibson, T.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
8. Corpet, F.: Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16 (1988) 10881-10890
9. Gotoh, O.: Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol. 264 (1996) 823-838
10. Notredame, C., Higgins, D.: SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res. 24 (1996) 1515-1524
11. Kim, J., Pramanik, S., Chung, M.: Multiple sequence alignment using simulated annealing. Comput. Appl. Biosci. 10 (1994) 419-426
12. Höhl, M., Kurtz, S., Ohlebusch, E.: Efficient multiple genome alignment. Bioinformatics 18 (2002) S312-S320
13. Morgenstern, B., Frech, K., Dress, A., Werner, T.: DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics 14 (1998) 290-294
14. Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., NISC Comparative Sequencing Program, Green, E.D., Sidow, A., Batzoglou, S.: LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13 (2003) 721-731
15. Bray, N., Pachter, L.: MAVID: Constrained ancestral alignment of multiple sequences. Genome Res. 14 (2004) 693-699
16. Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., Miller, W.: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14 (2004) 708-715
17. Schwartz, S., Elnitski, L., Li, M., Weirauch, M., Riemer, C., Smit, A., Program, N.C.S., Green, E.D., Hardison, R.C., Miller, W.: MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 31 (2003) 3518-3524
18. Kim, S.: Graph theoretic sequence clustering algorithms and their applications to genome comparison. In Wu, C.H., Wang, P., Wang, J.T.L., eds.: Computational Biology and Genome Informatics. World Scientific (2003)
19. Kim, S., Gopu, A.: Cluster utility: A new metric to guide sequence clustering. Technical report, School of Informatics, Indiana University (2004)
20. Miller, W.: Comparison of genomic DNA sequences: Solved and unsolved problems. Bioinformatics 17 (2001) 391-397