PACAS: pairwise comparisons of aligned subsequences

Abstract

Evaluation of conservation levels of alignments is a pivotal step for evolutionary analyses. Commonly used software to analyze alignments produce either site-by-site or overall measures of conservation without the ability of performing comparative analyses among sub-regions of the alignment. We have developed a stand-alone alignment analyzer (Pairwise Comparisons of Aligned Subsequences) that uses user-defined sub-regions to report various measures of conservation among pairs of sequences and between the sub-regions and the rest of the alignment. We then used this method to analyze the repetitive regions (low complexity regions; LCRs) of two genes in Plasmodium: AMA1 and CSP. We found that LCRs are not always associated with high entropy (low conservation) suggesting that some LCRs may be less likely to mutate than others. Availability and ImplementationPACAS is publicly available at https://github.com/BlabOaklandU/PACAS ContactFabia U. Battistuzzi battistu@oakland.edu Supplementary informationn/a