Maynooth University

Maynooth University ePrints and eTheses Archive

Maynooth University Library

SWAPSC: sliding window analysis procedure to detect selective constraints

Fares, Mario A (2004) SWAPSC: sliding window analysis procedure to detect selective constraints. Bioinformatics, 20 (16). pp. 2867-2868.

[img] Download (171kB)

Abstract

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 programestimates 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 nonsynonymous nucleotide substitutions. Thereafter, a statistical analysis is conducted to determine the optimum windowsize 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.

Item Type: Article
Keywords: sliding window, selective constraints,
Subjects: Science & Engineering > Biology
Item ID: 318
Depositing User: Dr. Mario Fares
Date Deposited: 15 Jun 2006
Journal or Publication Title: Bioinformatics
Publisher: Oxford University Press
Refereed: Yes
URI:

Repository Staff Only(login required)

View Item Item control page

Document Downloads

More statistics for this item...