A Survey on Genomic Sequence Alignment

PhD Qualifying Examination


Title: "A Survey on Genomic Sequence Alignment"

by

Mr. Ge BAI


Abstract:

Sequence alignment is a fundamental problem in bioinformatics.Given two 
genomic sequences or fragments (called reads), a sequence aligner locates 
similar regions between the two strings and matches them character by 
character to maximize some similarity measure.

This survey reviews a collection of representative algorithms in 
genomic sequence alignment. In particular, traditional alignment 
algorithms deal with long sequences and typically perform global 
alignment, i.e., matching the two entire sequences end to end. To reduce 
the search space, long read alignment often adopts heuristics. In 
comparison, recent techniques focus on short read alignment in which a 
large number of short reads of a length of 30-100 base pairs produced from 
next-generation sequencing (NGS) machines are matched against a long 
reference sequence. To speed up the local alignment of these short reads 
on the long sequence, indexing techniques based on the suffix tree or 
hashing have been proposed. As such, the two categories of algorithms 
share some commonality in the general problem handled but have their own 
strengths and weaknesses.


Date:			Tuesday, 29 January 2013

Time:                   2:00pm - 4:00pm

Venue:                  Room 3501
                         lifts 25/26

Committee Members:	Dr. Qiong Luo (Supervisor)
 			Prof. Dik-Lun Lee (Chairperson)
 			Prof. Frederick Lochovsky
 			Prof. Dimitris Papadias


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