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


CONCLUSIONS
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.
Crowe
Mark L
ML
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia. m.crowe@imb.uq.edu.au
D001483:Base Sequence; D002845:Chromatography / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D004252:DNA Mutational Analysis; D017931:DNA Primers; D003628:Database Management Systems; D030541:Databases, Genetic; D017353:Gene Deletion; D005838:Genotype; D006579:Heterozygote; D006720:Homozygote; D006801:Humans; D016247:Information Storage and Retrieval; D008969:Molecular Sequence Data; D016296:Mutagenesis; D020411:Oligonucleotide Array Sequence Analysis; D010363:Pattern Recognition, Automated; D017354:Point Mutation; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface
D017931:DNA Primers