ArticleBMC bioinformatics2005
SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis.Journal, genetic engineering & biotechnology · 2023Review
- Emergence of Ancylostoma caninum parasites with the benzimidazole resistance F167Y polymorphism in the US dog population.International journal for parasitology. Drugs and drug resistance · 2023Article
- A novel DNA methylation motif identified in Bacillus pumilus BA06 and possible roles in the regulation of gene expression.Applied microbiology and biotechnology · 2020Article
- Single-Nucleotide-Resolution Computing and Memory in Living Cells.Molecular cell · 2019Article
- Recurrent triploidy due to a failure to complete maternal meiosis II: whole-exome sequencing reveals candidate variants.Molecular human reproduction · 2015Article
- Rare allelic forms of PRDM9 associated with childhood leukemogenesis.Genome research · 2013Article
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- A substitution in the ligand binding domain of the porcine glucocorticoid receptor affects activity of the adrenal gland.PloS one · 2012Article
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- SNPmplexViewer--toward a cost-effective traceability system.BMC research notes · 2011Article
- Anthelmintic resistance: markers for resistance, or susceptibility?Parasitology · 2011Review
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Authors and funding
1 author.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThis 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.
resultsSeqDoC 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.
conclusionSeqDoC 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.
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Registered trials
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