QSVanalyser
Quantitative analysis of sequence variants
QSVanalyser is a program that allows rapid, user-controlled, batchwise analysis of DNA sequence traces for estimation of the relative proportions of two sequence variants (Quantitative Sequence Variants, QSVs).
QSVanalyser can process hundreds of sequence traces, and generates output files containing details of QSV ratios for individual samples, as well as summary statistics.
Examples of applications include:
- Estimation of proportions of somatic mutant sequences in tumour DNA
- Determination of genotypes at complex loci comprising 2–4 target copies per haploid genome
- Estimation of allele frequencies among pooled DNA samples
- Comparative analysis of sequence variants that define gene–pseudogene differences
- Estimation of relative allelic expression levels in RT-PCR products
A full description of QSVanalyser:
Carr IM, Robinson JI, Dimitriou R, Markham AF, Morgan AW, Bonthron DT (2009) Inferring relative proportions of DNA variants from sequencing electropherograms. Bioinformatics [Epub ahead of print] PMID: 19819885.
QSVanalyser runs on Microsoft Windows, using the .NET 2.0 environment.
The QSVanalyser downloads are here.
The QSVanalyser guide is here.
Citations
Carr IM, Robinson JI, Dimitriou R, Markham AF, Morgan AW, Bonthron DT.
Inferring relative proportions of DNA variants from sequencing electropherograms
Bioinformatics 2009 December 25:3244-3250