Name: ShortBRED
User manual || Tutorial
Description: ShortBRED is a system for profiling protein families of interest at very high specificity in shotgun meta’omic sequencing data. ShortBRED-Identify collapses proteins of interest into families, and then screens these families (as represented by consensus sequences) against 1) each other and 2) a comprehensive protein reference. ShortBRED-Identify then identifies short, distinguishing peptide sequences (“markers”) for each protein family. This process is performed once for a given set of proteins of interest to produce a reusable marker set (see below for examples of pre-computed markers). ShortBRED-Quantify then screens a metagenome or metatranscriptome against a given marker set to profile the presence/absence and relative abundance of the associated proteins.
Citation
Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C.
High-specificity targeted functional profiling in microbial communities with ShortBRED.
PLoS Comput Biol. 2015 Dec 18;11(12):e1004557.