ShortBRED specifications


Unique identifier OMICS_16928
Name ShortBRED
Alternative name Short Better Representative Extract Dataset
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Proteins of interest, reference set of proteins, short nucleotide reads.
Input format FASTA
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements Python, BLASTP, USEARCH, MUSCLE, CD-HIT
Maintained Yes



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  • person_outline Gautam Dantas <>

Publication for Short Better Representative Extract Dataset

ShortBRED institution(s)
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MI, USA; Broad Institute, Cambridge, MA, USA; Centre for Integrative Biology (CIBIO), University of Trento, Trento, Trentino, Italy; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MI, USA; Department of Biomedical Engineering, Washington University, St. Louis, MI, USA
ShortBRED funding source(s)
This work was supported by NIH grants of a Director’s New Innovator Award, DP2DK098089 and R01GM099538, the March of Dimes Foundation 6-FY12-394, NIH grants R01HG005969, NSF grant DBI-1053486, ARO grant W911NF-11-1-0473, Danone Research grant PLF-5972-GD, a Mr. and Mrs. Spencer T. Olin Fellowship at Washington University and a NSF Graduate Research Fellow (DGE-11143954).

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