Skip Navigation



Bioinformatics Advance Access published online on January 29, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth013
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
20/6/953    most recent
bth013v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Smoot, M. E.
Right arrow Articles by Pearson, W. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Smoot, M. E.
Right arrow Articles by Pearson, W. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received July 23, 2003
Accepted July 31, 2003

Article

Visualization of near optimal sequence alignments

Michael E. Smoot 1, Stephanie A. Guerlain 1, William R. Pearson 2*

1 Department of Systems and Information Engineering, University of Virginia, Charlottesville, VA 22908 USA
2 Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908 USA

* To whom correspondence should be addressed. E-mail: wrp{at}virginia.edu.


  Abstract

Motivation: Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for effectively finding the most biologically meaningful alignment in the potentially large set of options.

Results: We have developed web based software that displays near optimal or alternative alignments of two protein or DNA sequences as a continuous moving picture. A WWW interface to a C++ program generates suboptimal alignments, which are sent to a Java Applet, which displays them in a series of alignment frames. The Applet plots aligned residues so that consistently aligned regions remain at a fixed position on the display, while variable regions move. The display can be stopped to examine alignment details.

Availability: Available from: http://fasta.bioch.virginia.edu/noptalign. For source code contact the authors at: wrp@virginia.edu.


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
 IOVSHome page
A. M. Ozyildirim, G. J. Wistow, J. Gao, J. Wang, D. P. Dickinson, H. F. Frierson Jr, and G. W. Laurie
The Lacrimal Gland Transcriptome Is an Unusually Rich Source of Rare and Poorly Characterized Gene Transcripts
Invest. Ophthalmol. Vis. Sci., May 1, 2005; 46(5): 1572 - 1580.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Nozaki and M. Bellgard
Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties
Bioinformatics, April 15, 2005; 21(8): 1421 - 1428.
[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.