title: A frameshift error detection algorithm for DNA sequencing projects.
abstract: During the determination of DNA sequences, frameshift errors are not the most frequent but they are the most bothersome as they corrupt the amino acid sequence over several residues. Detection of such errors by sequence alignment is only possible when related sequences are found in the databases. To avoid this limitation, we have developed a new tool based on the distribution of non-overlapping 3-tuples or 6-tuples in the three frames of an ORF. The method relies upon the result of a correspondence analysis. It has been extensively tested on Bacillus subtilis and Saccharomyces cerevisiae sequences and has also been examined with human sequences. The results indicate that it can detect frameshift errors affecting as few as 20 bp with a low rate of false positives (no more than 1.0/1000 bp scanned). The proposed algorithm can be used to scan a large collection of data, but it is mainly intended for laboratory practice as a tool for checking the quality of the sequences produced during a sequencing project.
authors.affiliation: Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France.
authors.forename: G A
authors.initials: GA
authors.lastname: Fichant
authors.forename: Y
authors.initials: Y
authors.lastname: Quentin
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000235:genetics; D001426:Bacterial Proteins; D001483:Base Sequence; D004252:DNA Mutational Analysis; D004269:DNA, Bacterial / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D016002:Discriminant Analysis; D016368:Frameshift Mutation; D006801:Humans; D008969:Molecular Sequence Data; D010453:Peptide Synthases / Q000235:genetics; D016364:Reading Frames / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004271:DNA, Fungal; D010453:Peptide Synthases; C069542:surfactin synthetase