Automated whole-genome multiple alignment of rat, mouse, and human

Genome Research

Volumn 14, Issue 4, 2004, Pages 685-692

  Brudno, Michael ^a   Poliakov, Alexander ^b   Salamov, Asaf ^c,d   Cooper, Gregory M ^e   Sidow, Arend ^e,f   Rubin, Edward M ^b,c   Solovyev, Victor ^c,d   Batzoglou, Serafim ^a   Dubchak, Inna ^b,c  

^a Stanford University   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d SOFTBERRY INC   (United States)

^e STANFORD UNIVERSITY   (United States)

^f STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; AUTOANALYSIS; COMPUTER PROGRAM; CONTIG MAPPING; CONTROLLED STUDY; EXON; GENE MAPPING; GENE SEQUENCE; GENETIC CODE; GENOME ANALYSIS; HUMAN; HUMAN GENETICS; IMAGE DISPLAY; MAMMAL; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; ONLINE SYSTEM; PREDICTION; PRIORITY JOURNAL; RAT; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; SYNTENY;

ANIMALS; AUTOMATION; COMPUTATIONAL BIOLOGY; EXONS; GENOME; GENOME, HUMAN; HUMANS; MICE; PHYSICAL CHROMOSOME MAPPING; RATS; SEQUENCE ALIGNMENT; SOFTWARE; SYNTENY;

MAMMALIA;

EID: 1842717955     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2067704     Document Type: Article

References (29)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F.A., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., et al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. (this issue).
3. Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K.D., Ovcharenko, I., Pachter, L., and Rubin, E.M. 2003. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299: 1391-1394.
4. Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., Batzoglou, S., and NISC Comparative Sequencing Program. 2003a. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13: 721-731.
5. Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., and Batzoglou, S. 2003b. Glocal alignment: Finding rearrangements during alignment. Bioinformatics 19: 54i-62i.
6. Chiaramonte, F., Yap, V.B., and Miller, W. 2002. Scoring pairwise genomic sequence alignments. Pac. Symp. Biocomput. 115-126.
7. Cooper, G.M., Brudno, M., Green, E.D., Batzoglou, S., Sidow, A., and NISC Comparative Sequencing Program. 2003. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res. 13: 813-820.
8. Cooper, G.M., Brudno, M., Stone, E.A., Dubchak, I., Batzoglou, S., and Sidow, A. 2004. Characterization of evolutionary rates and constraints in three mammalian genomes Genome Res. (this issue).
9. Couronne, O., Poliakov, A., Bray, N., Ishkhanov, T., Ryaboy, D., Rubin, E.M., Pachter, L., and Dubchak, I. 2003. Strategies and tools for whole genome alignments. Genome Res. 13: 73-80.
10. Dubchak, I., Brudno, M., Pachter, L.S., Loots, G.G., Mayor, C., Rubin, E.M., and Frazer, K.A. 2000. Active conservation of noncoding sequences revealed by 3-way species comparisons. Genome Res. 10: 1304-1306.
11. Gottgens, B., Barton, L.M., Chapman, M.A., Sinclair, A.M., Knudsen, B., Grafham, D., Gilbert, J.G., Rogers, J., Bentley, D.R., and Green, A.R. 2002. Transcriptional regulation of the stem cell leukemia gene (SCL)-comparative analysis of five vertebrate SCL loci. Genome Res. 12: 749-759.
12. Hohl, M., Kurtz, S., and Ohlebusch, E. 2002. Efficient multiple genome alignment. Bioinformatics 18: S312-S320.
13. Hubbard, T., Barker, D., Birney, E., Cameron, G., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen, V., Down, T., et al. 2002. The Ensembl genome database project. Nucleic Acids Res. 30: 38-41.
14. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
15. Kent, W.J. 2002. BLAT - The BLAST-like alignment tool. Genome Res. 12: 656-664.
16. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Alan, M., Zahler, A.M., and Haussler, D. 2002. The Human Genome Browser at UCSC. Genome Res. 6: 996-1006.
17. Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. 2003. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. 100: 11484-11489.
18. Ma, B., Tromp, J., and Li, M. 2002. PatternHunter: Faster and more sensitive homology search. Bioinformatics 18: 440-445.
19. Mayor, C., Brudno, M., Schwartz, J.R., Poliakov, A., Rubin, E.M., Frazer, K.A., Pachter, L., and Dubchak, I. 2000. VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16: 1046-1047.
20. Rat Genome Sequencing Project Consortium. 2004. Genome sequence of the Brown Norway Rat yields insights into mammalian evolution. Nature (in press).
21. Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., and Miller, W. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13: 103-107.
22. Simon, A.L., Stone, E.A., and Sidow, A. 2002. Inference of functional regions in proteins by quantification of evolutionary constraints. Proc. Natl. Acad. Sci. 99: 2912-2917.
23. Solovyev, V.V. 2002. Finding genes by computer: Probabilistic and discriminative approaches. In Current topics in computational biology (eds. T. Jiang et al.), pp. 365-401. MIT Press, Cambridge, Massachusetts.
24. Sumiyama, K., Kim, C.B., and Ruddle, F.H. 2001. An efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships. Genomics 71: 260-262.
25. Thomas, J.W., Touchman, J.W., Blakesley, R.W., Bouffard, G.G., Beckstrom-Sternberg, S.M., Margulies, E.H., Blanchette, M., Siepel, A.C., Thomas, P.J., McDowell, J.C., et al. 2003. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424: 788-793.
26. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTALW: 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.
27. Vingron, M. and Waterman, M.S. 1994. Sequence alignment and penalty choice. Review of concepts, case studies and implications. J. Mol. Biol. 235: 1-12.
28. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
29. Yap, V.B. and Pachter, L. 2004. Identification of evolutionary hotspots in the rodent genomes. Genome Res. (this issue).