An introduction to the lagan alignment toolkit

Methods in Molecular Biology

Volumn 395, Issue , 2007, Pages 205-220

  Brudno, Michael ^a  

^a NONE

Author keywords

Alignment algorithms; Alignment visualization; Rearrangements

Indexed keywords

ALGORITHM; ARTICLE; GENETIC DATABASE; GENOME; INTERNET; SEQUENCE ALIGNMENT;

ALGORITHMS; DATABASES, GENETIC; GENOME; INTERNET; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); MAMMALIA;

EID: 36549067681     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-514-8:205     Document Type: Article

References (26)

1. Brudno, M., Do, C. B., Cooper, G. M, et al., and NISC Comparative Sequencing Program. (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721-731.
2. Schwartz, S., Elnitski, L., Li, M., et al., NISC Comparative Sequencing Program. (2003) MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 31, 3518-3524.
3. Darling, A. C., Mau, B., Blattner, F. R., and Perna, N. T. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394-1403.
4. Bray, N. and Pachter, L. (2004) MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14, 693-699.
5. Blanchette M, Kent WJ, Riemer C., et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715.
6. Batzoglou, S., Pachter, L., Mesirov, J. P., Berger, B., and Lander, E. S. (2000) Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 10, 950-958.
7. Bray, N., Dubchak, I., and Pachter, L. (2003) AVID: A global alignment program. Genome Res. 13, 97-102.
8. Schwartz, S., Kent, W. J., Smit, A., et al. (2003) Human-mouse alignments with BLASTZ. Genome Res. 13, 103-107.
9. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) 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, 4673-4680.
10. Morgenstern, B., Frech, K., Dress, A., and Werner, T. (1998) DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 14, 290-294.
11. Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
12. Bergman, C. M. and Kreitman, M. (2001) Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Res. 11, 1335-1345.
13. Brudno, M., Malde, S., Poliakov, A., et al. (2003) Glocal alignment: finding rearrangements during alignment. Bioinformatic 19, 54i-62i.
14. Brudno, M., Chapman, M., Gottgens, B., Batzoglou, S., and Morgenstern, B. (2003) Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics 4, 66.
15. Brudno, M., Poliakov, A., Salamov, A., et al. (2004) Automated whole-genome multiple alignment of rat, mouse, and human. Genome Res. 14, 685-692.
16. Kalafus, K. J., Jackson, A. R., Milosavljevic, A. (2004) Pash: efficient genomescale sequence anchoring by positional hashing. Genome Res. 14, 672-678.
17. Hubbard T, Andrews D, Caccamo M, et al. (2005) Ensembl 2005. Nucleic Acids Res. 33, D447-D453.
18. Mayor, C., Brudno, M., Schwartz, J. R., et al. (2000) VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16, 1046-1047.
19. Needleman, S. B. and Wunsch, C. D. (1970) An efficient method applicable to the search for similarities in the amino acid sequences of two proteins. J. MolI. Biol. 48, 444-453.
20. Delcher, A. L., Kasif, S., Fleischman, R., Peterson, J., White, O., and Salzberg, S. L. (1999) Alignment of whole genomes. Nucleic Acids Res. 27, 2369-2376.
21. Delcher, A. L., Phillippy, A., Carlton, J., and Salzberg, S. L. (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30, 2478-2483.
22. Kent, W, J. and Zahler, A. M. (2000) Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 10, 1115-1125.
23. Shah, N., Couronne, O., Pennacchio, L. A., et al. (2004) PhyloVISTA: an interactive visualization tool for multiple DNASequence aligameats. Bioinformatics 20, 636-643.
24. Montgomery, S. B., Astakhova, T., Bilenky, M., et al. (2004) Sockeye: a 3D environment for comparative genomics. Genome Res. 14, 956-962.
25. Couronne, O., Poliakov, A., Bray, N., et al. (2002) Strategies and tools for whole genome alignments. Genome Res. 13, 73-80.
26. Kent, J. (2002) BLAT: the BLAST-like alignment tool. Genome Res. 12, 656-664.