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A STUDY AND EVALUATION OF DNA- SEQUENCE-ASSEMBLY PROGRAMS

 

TITLE A STUDY AND EVALUATION OF DNA- SEQUENCE-ASSEMBLY PROGRAMS
AUTHOR ANUKOON WISITSORAAT
DEGREE MASTER OF SCIENCE PROGRAMME IN COMPUTER SCIENCE
FACULTY FACULTY OF SCIENCE
ADVISOR CHARNYOTE PLEUMPITIWIRIYAWEJ
CO-ADVISOR CHINAE THAMMARONGTHAM
 
ABSTRACT
DNA sequencing is one of the most important techniques for life science in the era of genome research. The limitations of current biochemical techniques make DNA assembly, particularly for large-scale genomes, highly challenging since it is complicated, time-consuming, and expensive. Computer technologies can be used to align and assemble fragments. The alignment and the assembly processes are complex and incompletely solved due to repeated patterns, DNA evolutions and sequencing errors. This thesis describes the underlying research, design and implementation of a new sequence assembly program, called SEQASS, to help in alignment and assembly of the whole genome sequences. SEQASS has been developed with respect to the framework presented in CAP3. Unlike CAP3, however, SEQASS uses BLAT, a BLAST-like tool, to accelerate pair-wise comparisons and improve assembly quality. SEQASS has been evaluated on the DNA sequences of mammal organisms, which were obtained from Genbank. The evaluation measurements include the total percent coverage, the total percent of identity, the number of good contigs, the average size of good contigs, the number of misassembled contigs, and the total run time. The output contig sequences were evaluated by comparing the sequences with the known whole genome input by BLAT. SEQASS performances were compared to other available programs including CAP3, CAP1, and TIGR. These evaluations showed that SEQASS is a useful tool in the alignment and assembly of whole sequence program and has good potential in the field of genome research.
KEYWORD DNA EQUENCE ASSEMBLY/DNA SEQUENCING/SEQASS/BLAT

 

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