Skip Navigation


Bioinformatics Advance Access originally published online on May 6, 2004
Bioinformatics 2004 20(16):2867-2868; doi:10.1093/bioinformatics/bth303
This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow All Versions of this Article:
20/16/2867    most recent
bth303v1
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 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 (12)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Fares, M. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fares, M. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.

Applications Note

SWAPSC: sliding window analysis procedure to detect selective constraints

Mario A. Fares

Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland

Received on April 15, 2004; revised on April 21, 2004; accepted on April 25, 2004
Advance Access Publication May 6, 2004

Summary: Sliding-window analysis procedure to detect selective constraints (SWAPSC) is a software system to dissect the constraints on the evolution of protein-coding genes. The program estimates rates of nucleotide substitutions at specific codon regions in each branch of a phylogenetic tree. The program uses several sets of simulated sequence alignments to estimate the probability of synonymous and non-synonymous nucleotide substitutions. Thereafter, a statistical analysis is conducted to determine the optimum window size to detect selective constraints. Finally, the optimum window size is slid along the real alignment and a test for significance of the estimated number of synonymous and non-synonymous nucleotide substitutions in each sliding step is conducted. A number of friendly useful output files is generated.

Availability: SWAPSC is available at http//www.may.ie/academic/biology/staff/mfmolecevolandbioinf.shtml. Distribution versions for both Linux and Windows operating systems are available, including manual and example files.

Contact: mario.fares{at}may.ie


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
 J. Virol.Home page
D. C. Tully and M. A. Fares
Shifts in the Selection-Drift Balance Drive the Evolution and Epidemiology of Foot-and-Mouth Disease Virus
J. Virol., January 15, 2009; 83(2): 781 - 790.
[Abstract] [Full Text] [PDF]

Home page
 J. Med. Genet.Home page
X-j Luo, H-b Diao, J-k Wang, H Zhang, Z-m Zhao, and B Su
Association of haplotypes spanning PDZ-GEF2, LOC728637 and ACSL6 with schizophrenia in Han Chinese
J. Med. Genet., December 1, 2008; 45(12): 818 - 826.
[Abstract] [Full Text] [PDF]

Home page
 Protein Eng Des SelHome page
B. Shen, J. Bai, and M. Vihinen
Physicochemical feature-based classification of amino acid mutations
Protein Eng. Des. Sel., January 1, 2008; 21(1): 37 - 44.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
Y. Radhakrishnan, M. A. Fares, F. S. French, and S. H. Hall
Comparative genomic analysis of a mammalian {beta}-defensin gene cluster
Physiol Genomics, August 20, 2007; 30(3): 213 - 222.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
V. Ruano-Rubio and M. A. Fares
Testing the Neutral Fixation of Hetero-Oligomerism in the Archaeal Chaperonin CCT
Mol. Biol. Evol., June 1, 2007; 24(6): 1384 - 1396.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
F. M. Codoner, M. A. Fares, and S. F. Elena
Adaptive Covariation between the Coat and Movement Proteins of Prunus Necrotic Ringspot Virus.
J. Virol., June 1, 2006; 80(12): 5833 - 5840.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. A. Fares and S. A. A. Travers
A Novel Method for Detecting Intramolecular Coevolution: Adding a Further Dimension to Selective Constraints Analyses
Genetics, May 1, 2006; 173(1): 9 - 23.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
S. A. A. Travers, M. J. O'Connell, G. P. McCormack, and J. O. McInerney
Evidence for Heterogeneous Selective Pressures in the Evolution of the env Gene in Different Human Immunodeficiency Virus Type 1 Subtypes
J. Virol., February 1, 2005; 79(3): 1836 - 1841.
[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.