Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Software

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

Mark L Crowe

Author Affiliations

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia

The Australian Research Council Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, Queensland 4072, Australia

BMC Bioinformatics 2005, 6:133  doi:10.1186/1471-2105-6-133

Published: 31 May 2005

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.