The Design And Implementation Of XAT Software System

The chief work of this thesis is to research the sequence alignment algorithm and implement XAT software which align cDNA/mRNA sequences with DNA sequences which can be not homologous with cDNA/mRNA sequences. It incorporates several heuristic techniques used in blastz and sim4 softwares, such as the cross-species method in blastz and the method positioning the border between intron and exon in sim4. It permits many cDNA/mRNA sequences aligning with whole genome, and offers the statistical value of the result. XAT provides configure file. And XAT is written in C language, so it's easy for migration.Firstly, this thesis introduces the concept of sequence alignment, it's mathematic model and some general algorithm to solve it. It mainly introduces some algorithms and the according softwares existed now.About XAT, it's meaning and algorithm are introduced in this thesis. And XAT has been implemented with C language. The interface,configure file and output formats are introduced too.The emphasis of this thesis is how to align cDNA/mRNA sequences with whole genome, how to increase the velocity, how to position the border between intron and exon and how to describe the result statistically. They are introduced in detail in this thesis.At last,using a method which is similar to that adopted in software genefinding, I analyze the result of XAT and compare it with some other softwares.