Trace alignment and some of its applications

Abstract

Motivation: Extra useful information can be extracted from a DNA chromatogram trace, over that contained in the base-called DNA sequence. Many sequencing applications can benefit from examination of these traces. Results: An algorithm, based on dynamic programming, for aligning a DNA chromatogram to a DNA sequence is described and implemented. Its applications to vector clipping, EST alignment and mutation detection are discussed. Availability: The package is available by anonymous ftp from ftp://ftp.sanger.ac.uk/pub/badger/tracetools.tar.Z.