Assessing the efficiency of multiple sequence alignment programs.

ABSTRACT:

Background

Multiple sequence alignment (MSA) is an extremely useful tool for molecular and evolutionary biology and there are several programs and algorithms available for this purpose. Although previous studies have compared the alignment accuracy of different MSA programs, their computational time and memory usage have not been systematically evaluated. Given the unprecedented amount of data produced by next generation deep sequencing platforms, and increasing demand for large-scale data analysis, it is imperative to optimize the application of software. Therefore, a balance between alignment accuracy and computational cost has become a critical indicator of the most suitable MSA program. We compared both accuracy and cost of nine popular MSA programs, namely CLUSTALW, CLUSTAL OM

SUBMITTER: Pais FS 

PROVIDER: S-EPMC4015676 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature