SEQAID: a DNA sequence assembling program based on a mathematical model

Abstract

A program package, called SEQAID, to support DNA sequencing is presented. The program automatically assembles long DNA sequences from short fragments with minimal user interaction. Various tools for controlling the assembling process are also available. The main novel features of the system are that SEQAID implements several new well-behaved algorithms based on a mathematical model of the problem. It also utilizes available information on restriction fragments to detect illegitimate overlaps and to find relationships between separately assembled sequence blocks. Experiences with the system are reported including an extremely pathological real sequence which offers an interesting benchmark for this kind of programs.