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.
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Release files for shortbred 0.9.5
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Source distribution (sdist)
| File | Size | Uploaded | |
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| shortbred-0.9.5.tar.gz | 42.3 kB | Details |
Release files / shortbred-0.9.5.tar.gz
| Download URL | shortbred-0.9.5.tar.gz |
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| Size | 42.3 kB |
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a6ac09b858f14e2c0b8622b122ec91e5d02d32c12429cad66626d7ef26df10d5
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twine/3.1.1 pkginfo/1.5.0.1 requests/2.23.0 setuptools/47.1.1.post20200529 requests-toolbelt/0.9.1 tqdm/4.46.0 CPython/3.6.10
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