Multiple Sequence Alignment A survey of the various programs available and application of MSA in addressing certain biological problems. Jeff Mower Kiran Annaiah. Sequence Comparison. Aligning two sequences is the cornerstone of Bioinformatics.
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Jeff Mower
Kiran Annaiah
– based on seq. similarity we can identify unknown biological relationship
could be highly significant if same residues are conserved
in other distantly related sequences
Given n sequences , consider the following cases:
http://www.math.tau.ac.il/~rshamir/algmb/00/scribe00/html/lec06/node11.html
BAliBASE  each set Reference set 1
Scores based on core blocks(V1) each set
Scores based on fulllength alignment(V1)
Median score for each set Reference set 2
Median score for aligning subgroups of sequences in each set Reference set 3
Median score for N/C terminal extensions – each set Reference set 4
Median score for internal insertions – each set Reference set 5
Results of BAliBASE testing each set
CPU time consumed by each program to align sets of increasingly long sequences
(Baldauf 2003)
(Baldauf 2003)
Rat
K RatKan =
K HumKan =
+
+
Human
K RatKan  K HumKan =

Kangaroo
(Thomas increasingly long sequenceset al. 2003)
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