TURNIP: Tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence

Robert P. Davey; Stephen A. James; Jo Dicks; Ian N. Roberts

doi:10.1093/bioinformatics/btq557

TURNIP: Tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence

Robert P. Davey^*, Stephen A. James, Jo Dicks, Ian N. Roberts

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

Abstract

Summary: 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.

Original language	English
Article number	btq557
Pages (from-to)	2908-2909
Number of pages	2
Journal	Bioinformatics
Volume	26
Issue number	22
DOIs	https://doi.org/10.1093/bioinformatics/btq557
Publication status	Published - Nov 2010
Externally published	Yes

Bibliographical note

Funding Information:
Funding: Biotechnology and Biological Sciences Research Council Tools and Resources Development Fund project no. BB/G000441/1 (to R.P.D.); BBSRC (to S.A.J., I.N.R., J.D.).

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title = "TURNIP: Tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence",

abstract = "Summary: 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.",

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doi = "10.1093/bioinformatics/btq557",

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AU - Roberts, Ian N.

N1 - Funding Information: Funding: Biotechnology and Biological Sciences Research Council Tools and Resources Development Fund project no. BB/G000441/1 (to R.P.D.); BBSRC (to S.A.J., I.N.R., J.D.).

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TURNIP: Tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence

Abstract

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