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BEAN-Counter Quantitative Scoring of Chemical-Genetic Interactions

Technology #20170001

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BEAN-Counter Commercial Research License - Large Team
$4,000.00
BEAN-Counter Commercial Research License - Small Team
$2,500.00
BEAN-Counter Commercial Research License (Trial)
$0.00
BEAN-Counter Academic Research License
$0.00
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Chemical-genetic InteractionsChemical GenomicsS. cerevisiae Yeast
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Researchers
Chad Myers
Associate Professor, Computer Science and Engineering
External Link (www.cs.umn.edu)
Scott Simpkins
Graduate School Fellow, Computer Science and Engineering
Managed By
Andrew Morrow
Technology Licensing Officer

Chemical Genomics Barcode Sequencing

BEAN-counter (Barcoded Experiment Analysis from Next-generation sequencing) software is a pipeline for quantitative scoring of chemical-genetic interactions from sequencing-based chemical-genetic interaction screens. It provides a complete toolset for processing multiplexed sequencing data from barcoded mutant pools into chemical-genetic interaction profiles, based on these basic inputs: 1) sequences of multiplexed, pooled PCR products amplified from barcoded strain pools; 2) a mapping from the barcode sequences to the strain identities; and 3) a mapping from the index (multiplex) tags to the identities of the chemical conditions. In addition, post-processing normalization steps perform quality control corrections for biases and effects observable in large-scale chemical genomic screens.

Chemical-Genetic Interaction Scoring and Post-processing

BEAN-counter is a unique tool that implements both the scoring and post-processing steps in a single package. It is a full-featured pipeline that not only converts the raw data into chemical-genetic interaction scores but also performs well at scale and implements, featuring: 1) quality control checks on the strains and conditions; 2) normalization steps to remove technical artifacts and systematic biases especially visible in large-scale screens; and 3) methods to visualize the data at every step during its processing. BEAN-counter computes chemical-genetic interaction z-scores based on estimates of the standard deviation as a function of observed strain abundance.

BENEFITS AND FEATURES:

  • Quantitative scoring of chemical-genetic interactions from sequencing-based chemical-genetic interaction screens
  • Corrects for biases and effects observable in large-scale chemical genomic screens
  • Provides scoring and post-processing in a single package
  • Computes chemical-genetic interaction z-scores

APPLICATIONS:

  • Chemical/pharmaceutical companies who perform chemical genomic experiments to determine compounds' modes-of-action.
  • Processing raw data from chemical genomic experiments

Phase of Development Working prototype