Focus of this presentation
   Meaning of Sequence Alignment
   Global and Local Alignment of Sequences
   Pairwise and Multiple Sequence Alignment
   Scoring of Aligned Sequences
   Significance of Sequence Alignment
   Sequence Alignment Programs
   Tutorials
        Sequence Alignment
  • Sequence alignment is the procedure of comparing 
   two (pair-wise alignment) or more (multiple 
   sequence alignment) sequences by searching for a 
   series of individual characters or character patterns 
   that are in the same order in the sequences.
  • Probably the most common experiment done in 
   modern day biology
  • It is considered an experiment because you don’t 
   have an idea of the outcome with the sequence
  • It generates result that leads to a conclusion 
   or further experiment
  • There are two types of sequence alignment, 
   global and local as illustrated in figure 1.
  Figure 1. Distinction between global and local 
  alignments of two sequences
  Global  alignment  (Needleman  and  Wunsch,  1970)
  • One approach for searching a query sequence is to 
   align the entire sequence against all sequences in a 
   database
  • Attempt is made to align the entire sequence using 
   as many characters as possible, up to both ends of 
   each sequence.
  • Sequences that are quiet similar and approximately 
   the same length are suitable candidates. 
  • This approach is very slow and hence impractical