Physical Sciences and Mathematics Commons^™

Exact Genome Alignment, Nandini Ghosh

Theses

The increase in the volume of genomic data due to the decrease in the cost of whole genome sequencing techniques has opened up new avenues of research in the field of Bioinformatics, like comparative genomics and evolutionary dynamics. The fundamental task in these studies is to align the genome sequences accurately. Sequence alignment helps to identify regions of similarity between the sequences to establish their functional, evolutionary and structural relationship. The thesis investigates the performance of two sequence alignment programs LASTZ, a hash table based faster method and SSEARCH, a slower but more rigorous Smith-Waterman based approach, on whole genome …

Fast Program For Sequence Alignment Using Partition Function Posterior Probabilities, Meera Prasad

Theses

The key requirements of a good sequence alignment tool are high accuracy and fast execution. The existing Probalign program is a highly accurate tool for sequence alignment of both proteins and nucleotides. However, the time for execution is fairly high. The focus is therefore, to reduce the running time of the existing version of Probalign, maintaining its current accuracy level.

The thesis conducts a detail analysis of the performance of Probalign to bring down the running time of the existing code. A modified version of Probalign, Version 1.4 is released. A new program for sequence alignment with faster computation is …