Special Issue Papers |
The many faces of sequence alignment
Received his PhD from MIT in 2000. He is an Assistant Professor of Computer Science at Stanford, and his research focus is computational biology.
Serafim Batzoglou, Department of Computer Science, Stanford University, James H. Clark Center, 318 Campus Drive, RM S-266, Stanford, CA 94305—5428, USA E-mail: serafim{at}cs.stanford.edu
Starting with the sequencing of the mouse genome in 2002, we have entered a period where the main focus of genomics will be to compare multiple genomes in order to learn about human biology and evolution at the DNA level. Alignment methods are the main computational component of this endeavour. This short review aims to summarise the current status of research in alignments, emphasising large-scale genomic comparisons and suggesting possible directions that will be explored in the near future.
Keywords: sequence alignment, local alignment, multiple alignment, synteny detection, rearrangements, hidden Markov model
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  G. M. Cooper and C. D. Brown Qualifying the relationship between sequence conservation and molecular function Genome Res., February 1, 2008; 18(2): 201 - 205. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Lunter, A. Rocco, N. Mimouni, A. Heger, A. Caldeira, and J. Hein Uncertainty in homology inferences: Assessing and improving genomic sequence alignment Genome Res., February 1, 2008; 18(2): 298 - 309. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. S. Srinivasan, N. H. Shah, J. A. Flannick, E. Abeliuk, A. F. Novak, and S. Batzoglou Current progress in network research: toward reference networks for key model organisms Brief Bioinform, September 1, 2007; 8(5): 318 - 332. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. S. Schwartz and L. Pachter Multiple alignment by sequence annealing Bioinformatics, January 15, 2007; 23(2): e24 - e29. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Flannick, A. Novak, B. S. Srinivasan, H. H. McAdams, and S. Batzoglou Graemlin: General and robust alignment of multiple large interaction networks Genome Res., September 1, 2006; 16(9): 1169 - 1181. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Bhasi, L. Zhang, D. Brazeau, A. Zhang, and M. Ramanathan VizStruct for visualization of genome-wide SNP analyses Bioinformatics, July 1, 2006; 22(13): 1569 - 1576. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. N. Dewey and L. Pachter Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Hum. Mol. Genet., April 15, 2006; 15(suppl_1): R51 - R56. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Canaran, L. Stein, and D. Ware Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support Bioinformatics, April 1, 2006; 22(7): 885 - 886. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Huang, D. M. Umbach, and L. Li Accurate anchoring alignment of divergent sequences Bioinformatics, January 1, 2006; 22(1): 29 - 34. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. M. Schwarz, I. Antoshechkin, C. Bastiani, T. Bieri, D. Blasiar, P. Canaran, J. Chan, N. Chen, W. J. Chen, P. Davis, et al. WormBase: better software, richer content Nucleic Acids Res., January 1, 2006; 34(suppl_1): D475 - D478. [Abstract] [Full Text] [PDF]
|
|