# About the ShortBRED category

**URL:** <https://forum.biobakery.org/t/about-the-shortbred-category/45>\
**Category:** ShortBRED\
**Created:** [November 12, 2019, 5:05pm UTC](https://forum.biobakery.org/t/about-the-shortbred-category/45 "2019-11-12T17:05:46Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [November 12, 2019, 5:05pm UTC](https://forum.biobakery.org/t/about-the-shortbred-category/45/1 "2019-11-12T17:05:46Z")

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Name: [**ShortBRED**](https://huttenhower.sph.harvard.edu/shortbred)  
[User manual](https://bitbucket.org/biobakery/shortbred/wiki/Home) || [Tutorial](https://bitbucket.org/biobakery/biobakery/wiki/shortbred)

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](https://huttenhower.sph.harvard.edu/shortbred#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.](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004557)  
PLoS Comput Biol. 2015 Dec 18;11(12):e1004557.