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

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

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

Author(s) -

Robert Davey,

Stephen A. James,

Jo Dicks,

Ian N. Roberts

Publication year - 2010

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btq557

Subject(s) - indel , genetics , biology , perl , genome , genbank , computational biology , dna sequencing , single nucleotide polymorphism , gene , computer science , programming language , genotype

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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