High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.

ABSTRACT: Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, and short read lengths can result in spurious hits to unrelated proteins (loss of specificity). We developed ShortBRED (Short, Better Representative Extract Dataset) to address these challenges, facilitating fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i) a method that reduces reference proteins of interest to short, highly representative amino acid sequences ("markers") and (ii) a search step that maps reads to these markers to quantify the relative abundance of their associated proteins. After evaluating ShortBRED o

SUBMITTER: Kaminski J 

PROVIDER: S-EPMC4684307 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature