%0 Journal Article
%T galign: A Tool for Rapid Genome Polymorphism Discovery
%A Shai Shaham
%J PLOS ONE
%D 2009
%I Public Library of Science (PLoS)
%R 10.1371/journal.pone.0007188
%X Background Highly parallel sequencing technologies have become important tools in the analysis of sequence polymorphisms on a genomic scale. However, the development of customized software to analyze data produced by these methods has lagged behind. Methods/Principal Findings Here I describe a tool, ¡®galign¡¯, designed to identify polymorphisms between sequence reads obtained using Illumina/Solexa technology and a reference genome. The ¡®galign¡¯ alignment tool does not use Smith-Waterman matrices for sequence comparisons. Instead, a simple algorithm comparing parsed sequence reads to parsed reference genome sequences is used. ¡®galign¡¯ output is geared towards immediate user application, displaying polymorphism locations, nucleotide changes, and relevant predicted amino-acid changes for ease of information processing. To do so, ¡®galign¡¯ requires several accessory files easily derived from an annotated reference genome. Direct sequencing as well as in silico studies demonstrate that ¡®galign¡¯ provides lesion predictions comparable in accuracy to available prediction programs, accompanied by greater processing speed and more user-friendly output. We demonstrate the use of ¡®galign¡¯ to identify mutations leading to phenotypic consequences in C. elegans. Conclusion/Significance Our studies suggest that ¡®galign¡¯ is a useful tool for polymorphism discovery, and is of immediate utility for sequence mining in C. elegans.
%U http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007188