SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms

Crowe, M. L. (2005) SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms. Bmc Bioinformatics, 6 133: . doi:10.1186/1471-2105-6-133


Author Crowe, M. L.
Title SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms
Journal name Bmc Bioinformatics   Check publisher's open access policy
ISSN 1471-2105
Publication date 2005
Sub-type Article (original research)
DOI 10.1186/1471-2105-6-133
Open Access Status DOI
Volume 6
Issue 133
Total pages 12
Place of publication London
Publisher Biomed Central Ltd
Collection year 2005
Language eng
Subject C1
270899 Biotechnology not elsewhere classified
730305 Diagnostic methods
Abstract Background: This paper describes SeqDoC, a simple, web-based tool to carry out direct comparison of ABI sequence chromatograms. This allows the rapid identification of single nucleotide polymorphisms (SNPs) and point mutations without the need to install or learn more complicated analysis software. Results: SeqDoC produces a subtracted trace showing differences between a reference and test chromatogram, and is optimised to emphasise those characteristic of single base changes. It automatically aligns sequences, and produces straightforward graphical output. The use of direct comparison of the sequence chromatograms means that artefacts introduced by automatic base-calling software are avoided. Homozygous and heterozygous substitutions and insertion/deletion events are all readily identified. SeqDoC successfully highlights nucleotide changes missed by the Staden package 'tracediff' program. Conclusion: SeqDoC is ideal for small-scale SNP identification, for identification of changes in random mutagenesis screens, and for verification of PCR amplification fidelity. Differences are highlighted, not interpreted, allowing the investigator to make the ultimate decision on the nature of the change.
Keyword Biochemical Research Methods
Biotechnology & Applied Microbiology
Evolution
Disease
Genes
Q-Index Code C1
Additional Notes Article number 133

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2006 Higher Education Research Data Collection
Institute for Molecular Bioscience - Publications
 
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Created: Wed, 15 Aug 2007, 06:04:42 EST