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Nucleic Acids Research, 1995, Vol. 23, No. 15 2900-2908
© 1995

COMPUTATIONAL BIOLOGY

A frameshift error detection algorithm for DNA sequencing projects

Gwennaele A. Flchant* and Yves Quentln1

Institut de Geèneètique et Microbiologie, Universoteé Paris-Sud Baätiment 400, 9405 Orsay Cedex, France 1Laboratorie de Chimie Bacteèrienne CNRS, 3 Chemin Joseph Aiguier, BP 7, 13277 Marseille Cedex 9, France

*To Whom correspondence should be addressed

Received April 24, 1995. Accepted June 20, 1995.

During the determination of DNA sequences, frameshif 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 subtllls and Saccharomyces cerevlsiae 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.


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