Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees.

ABSTRACT:

Motivation

Large multiple sequence alignments (MSAs), consisting of thousands of sequences, are becoming more and more common, due to advances in sequencing technologies. The MAFFT MSA program has several options for building large MSAs, but their performances have not been sufficiently assessed yet, because realistic benchmarking of large MSAs has been difficult. Recently, such assessments have been made possible through the HomFam and ContTest benchmark protein datasets. Along with the development of these datasets, an interesting theory was proposed: chained guide trees increase the accuracy of MSAs of structurally conserved regions. This theory challenges the basis of progressive alignment methods and needs to be examined by being compared with other known methods including com

SUBMITTER: Yamada KD 

PROVIDER: S-EPMC5079479 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature