Related Experiment Video
Updated: Jun 8, 2026
A Method to Study the C924T Polymorphism of the Thromboxane A2 Receptor Gene
Published on: April 1, 2019
TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence
Robert P Davey1, Stephen A James, Jo Dicks
1National Collection of Yeast Cultures, Institute of Food Research and Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UA, UK. robert.davey@bbsrc.ac.uk
Unlabelled:
TURNIP comprises a suite of Perl scripts and modules that facilitates the resolution of microheterogeneity within hard-to-assemble repetitive DNA sequences. TURNIP was originally developed for the Saccharomyces Genome Resequencing Project (SGRP) within which the ribosomal DNA (rDNA) of 36 strains of S.cerevisiae were analysed to investigate the occurrence of potential polymorphisms. Here, 'partially resolved SNPs', or pSNPs, as well as indels, were found to be far more prevalent than previously suspected. More generally, the TURNIP software ascertains degrees of variation between large tandem repeats within a single locus, offering insights into mechanisms of genome stability and gene conversion in any organism for which genome sequence data are available.
Availability:
The TURNIP source code, results files and online help are available at http://www.ncyc.co.uk/software/turnip.html.
