Journal article
Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, Vol.136, e57802
06/01/2018
DOI: 10.3791/57802
PMCID: PMC6102007
PMID: 30010636
Abstract
We have adapted the yeast 2-hybrid assay to simultaneously uncover dozens of transient and static protein interactions within a single screen utilizing high-throughput short-read DNA sequencing. The resulting sequence datasets can not only track what genes in a population that are enriched during selection for positive yeast 2-hybrid interactions, but also give detailed information about the relevant subdomains of proteins sufficient for interaction. Here, we describe a full suite of stand-alone software programs that allow non-experts to perform all the bioinformatics and statistical steps to process and analyze DNA sequence fastq files from a batch yeast 2-hybrid assay. The processing steps covered by these software include: 1) mapping and counting sequence reads corresponding to each candidate protein encoded within a yeast 2-hybrid prey library; 2) a statistical analysis program that evaluates the enrichment profiles; and 3) tools to examine the translational frame and position within the coding region of each enriched plasmid that encodes the interacting proteins of interest.
Details
- Title: Subtitle
- Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
- Creators
- Venkatramanan Krishnamani - University of IowaTabitha A. Peterson - University of IowaRobert C. Piper - University of IowaMark A. Stamnes - University of Iowa
- Resource Type
- Journal article
- Publication Details
- JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, Vol.136, e57802
- Publisher
- Journal Of Visualized Experiments
- DOI
- 10.3791/57802
- PMID
- 30010636
- PMCID
- PMC6102007
- ISSN
- 1940-087X
- eISSN
- 1940-087X
- Number of pages
- 10
- Grant note
- 1517110 / NSF Research Project R01GM058202 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) P30CA086862 / NATIONAL CANCER INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI) 1517110 / Direct For Biological Sciences; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) R21EB021870 / NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Biomedical Imaging & Bioengineering (NIBIB) R21 EB021870-01A1 / National Institutes of Health : NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA
- Language
- English
- Date published
- 06/01/2018
- Academic Unit
- Molecular Physiology and Biophysics; Medicine Administration; Internal Medicine
- Record Identifier
- 9984297608102771
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