PALADIN: protein alignment for functional profiling whole metagenome shotgun data.

ABSTRACT:

Motivation

Whole metagenome shotgun sequencing is a powerful approach for assaying the functional potential of microbial communities. We currently lack tools that efficiently and accurately align DNA reads against protein references, the technique necessary for constructing a functional profile. Here, we present PALADIN-a novel modification of the Burrows-Wheeler Aligner that provides accurate alignment, robust reporting capabilities and orders-of-magnitude improved efficiency by directly mapping in protein space.

Results

We compared the accuracy and efficiency of PALADIN against existing tools that employ nucleotide or protein alignment algorithms. Using simulated reads, PALADIN consistently outperformed the popular DNA read mappers BWA and NovoAlign in detected proteins, p

SUBMITTER: Westbrook A 

PROVIDER: S-EPMC5423455 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature