Skip Navigation

This Article
Right arrow Full Text (Print PDF)
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 Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Chao, K.-M.
Right arrow Articles by Miller, W.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Chao, K.-M.
Right arrow Articles by Miller, W.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© Oxford University Press

Locating well-conserved regions within a pairwise alignment

Kun-Mao Chao , Ross C. Hardison 1,2 and Webb Miller 2

Department of Computer Science University Park, PA 16802, USA
1Department of Molecular and Cell Biology University Park, PA 16802, USA
2Center for Gene Regulation, The Pennsylvania State University University Park, PA 16802, USA

Within a single alignment of two DNA sequences or two protein sequences, some regions may be much better conserved than others. Such strong conservation may reveal a region that possesses an important function. When alignments are so long that it is infeasible, or at least undesirable, to inspect them in complete detail, it is helpful to have an automatic process that computes information about the varying degree of conservation along the alignment and displays the information in a graphical representation that is readily assimilated. This paper presents methods for computing several such ‘robustness measures’ at each position of a given alignment. These methods are all very space-efficient; they use only space proportional to the sum of the two sequence lengths. To illustrate their effectiveness, one of the methods is used to locate particularly well-conserved regions in the ß-globin gene locus control region and in the 5' flank of the {gamma}-globin gene.

Received on April 25, 1992; accepted on January 5, 1993

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
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]

Home page
 BioinformaticsHome page
A. J. Bordner and R. Abagyan
REVCOM: a robust Bayesian method for evolutionary rate estimation
Bioinformatics, May 15, 2005; 21(10): 2315 - 2321.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
C. B. Do, M. S.P. Mahabhashyam, M. Brudno, and S. Batzoglou
ProbCons: Probabilistic consistency-based multiple sequence alignment
Genome Res., February 1, 2005; 15(2): 330 - 340.
[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.