Yost Lab Bioinformatics Tools
Supported by the B2B Consortium Grant:
https://www.benchtobassinet.com
Quick Links to Yost Lab Shiny Apps
Poly Peak Parser: http://yosttools.genetics.utah.edu/PolyPeakParser
Zebrafish Embryonic Heart Timecourse App: http://yosttools.genetics.utah.edu/zebrafish_heart_timecourse
Founder Principle-Driven Enrichment Calculator: http://yosttools.genetics.utah.edu/FPE_calculator
Poly Peak Parser
Background: Genome editing techniques, including ZFN, TALEN and CRISPR, have created a need to rapidly screen many F1 individuals to identify carriers of short indels and determine the sequences of the mutations. Current techniques require multiple clones of the targeted region to be sequenced for each individual, which is inefficient when many individuals must be analyzed. Direct Sanger sequencing of a PCR amplified region surrounding the target site is efficient, but Sanger sequencing genomes heterozygous for an indel results in a string of double peaks due to the mismatched region.
Results: In order to facilitate indel identification, we developed an online tool called Poly Peak Parser that is able to separate chromatogram data containing ambiguous base calls into wild-type and mutant allele sequences, revealing the nature of the indel from a single sequencing run per individual performed directly on a PCR product spanning the targeted site, without cloning.
Conclusions: The method and algorithm described here facilitate rapid identification and sequence characterization of heterozygous mutant carriers generated by genome editing. Although designed for screening F1 individuals after genome editing, this tool can also be used to identify heterozygous indels in many contexts.
Please cite:
Hill JT, Demarest BL, Bisgrove BW, Su YC, Smith M, Yost HJ. (2014) Poly Peak Parser: Method and software for identification of unknown indels using Sanger Sequencing of PCR products. Developmental Dynamics. PMID: 25160973
Go to PolyPeakParser web tool:
http://yosttools.genetics.utah.edu/PolyPeakParser
The code used to make PolyPeakParser is available as the “sangerseqR” bioconductor package:
https://www.bioconductor.org/packages/release/ bioc/html/sangerseqR.html
The sangerseqR package has been used to create a tool to estimate the frequency of somatic indels in TALEN or CRISPR injected animals or cell lines:
Users looking for a reference-free method should look into Indelligent:
http://dmitriev.speciesfile.org/indel.asp
Founder Principle-Driven Enrichment Calculator
Founder principle-driven enrichment (FPE) is a method that allows isolation of rare BAC recombinants (as rare as 1:10,000 to 1:100,000) without using selectable markers. The web-based calculator presented here enables users to easily determine all possible optimal FPE parameters for any desired cost function, i.e. the specific working conditions.
Please cite:
George T. Lyozin, Paul C. Bressloff, Amit Kumar, Yasuhiro Kosaka, Bradley L. Demarest, H. Joseph Yost, Michael R. Kuehn, and Luca Brunelli (2014) Isolation of rare recombinants without using selectable markers for one-step seamless BAC mutagenesis. Nature Methods. PMID: 25028895
Go to FPE Calculator web tool: