Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (343K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (29)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Bray, N.
Right arrow Articles by Pachter, L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bray, N.
Right arrow Articles by Pachter, L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 13 3525-3526
© 2003 Oxford University Press

MAVID multiple alignment server

Nicolas Bray and Lior Pachter*

Department of Mathematics, 970 Evans Hall, UC Berkeley, Berkeley, CA 94720, USA

*To whom correspondence should be addressed. Tel: +1 510 642 2028; Fax: +1 510 642 8204; Email: lpachter{at}math.berkeley.edu

MAVID is a multiple alignment program suitable for many large genomic regions. The MAVID web server allows biomedical researchers to quickly obtain multiple alignments for genomic sequences and to subsequently analyse the alignments for conserved regions. MAVID has been successfully used for the alignment of closely related species such as primates and also for the alignment of more distant organisms such as human and fugu. The server is fast, capable of aligning hundreds of kilobases in less than a minute. The multiple alignment is used to build a phylogenetic tree for the sequences, which is subsequently used as a basis for identifying conserved regions in the alignment. The server can be accessed at http://baboon.math.berkeley.edu/mavid/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome ResHome page
M. Irimia, S. W. Roy, D. E. Neafsey, J. F. Abril, J. Garcia-Fernandez, and E. V. Koonin
Complex selection on 5' splice sites in intron-rich organisms
Genome Res., November 1, 2009; 19(11): 2021 - 2027.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
A. Bashir, C. Ye, A. L. Price, and V. Bafna
Orthologous repeats and mammalian phylogenetic inference
Genome Res., July 1, 2005; 15(7): 998 - 1006.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
Y. Zhang and M. S. Waterman
An Eulerian path approach to local multiple alignment for DNA sequences
PNAS, February 1, 2005; 102(5): 1285 - 1290.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
D. Boffelli, C. V. Weer, L. Weng, K. D. Lewis, M. I. Shoukry, L. Pachter, D. N. Keys, and E. M. Rubin
Intraspecies sequence comparisons for annotating genomes
Genome Res., December 1, 2004; 14(12): 2406 - 2411.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
A. Coventry, D. J. Kleitman, and B. Berger
MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure
PNAS, August 17, 2004; 101(33): 12102 - 12107.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
A. C.E. Darling, B. Mau, F. R. Blattner, and N. T. Perna
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
Genome Res., July 1, 2004; 14(7): 1394 - 1403.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
V. B. Yap and L. Pachter
Identification of Evolutionary Hotspots in the Rodent Genomes
Genome Res., April 1, 2004; 14(4): 574 - 579.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
N. Bray and L. Pachter
MAVID: Constrained Ancestral Alignment of Multiple Sequences
Genome Res., April 1, 2004; 14(4): 693 - 699.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. Blanchette, W. J. Kent, C. Riemer, L. Elnitski, A. F.A. Smit, K. M. Roskin, R. Baertsch, K. Rosenbloom, H. Clawson, E. D. Green, et al.
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
Genome Res., April 1, 2004; 14(4): 708 - 715.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Siepel and D. Haussler
Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood
Mol. Biol. Evol., March 1, 2004; 21(3): 468 - 488.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. B. Major and D. A. Jones
Identification of a gadd45{beta} 3' Enhancer That Mediates SMAD3- and SMAD4-dependent Transcriptional Induction by Transforming Growth Factor {beta}
J. Biol. Chem., February 13, 2004; 279(7): 5278 - 5287.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
E. H. Margulies, M. Blanchette, NISC Comparative Sequencing Program, D. Haussler, and E. D. Green
Identification and Characterization of Multi-Species Conserved Sequences
Genome Res., December 1, 2003; 13(12): 2507 - 2518.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.