Transcript Slide 1

Multiple Sequence
Alignment
Multiple Alignment- First pair
• Align the two most closely-related
sequences first.
• This alignment is then ‘fixed’ and will
never change. If a gap is to be introduced
subsequently, then it will be introduced in
the same place in both sequences, but
their relative alignment remains
unchanged.
ClustalW- Decision time
• Consult the guide tree to see what alignment is
performed next.
– Align a third sequence to the first two
Or
– Align two entirely different sequences to
each other.
Option 1
Option 2
ClustalW- Alternative 1
If the situation arises where
a third sequence is aligned
to the first two, then when a
gap has to be introduced to
improve the alignment, each
of these two entities are
treated as two single
sequences.
+
ClustalW- Alternative 2
• If, on the other hand, two
separate sequences have to
be aligned together, then the
first pairwise alignment is
placed to one side and the
pairwise alignment of the
other two is carried out.
+
ClustalW-Good points/Bad points
• Advantages:
– Speed
• Disadvantages:
– No way of quantifying whether or not
the alignment is good.
– No way of knowing if the alignment is
‘correct’.
ClustalW - Local Minimum
• Potential problems:
– Local minimum problem. If an error is
introduced early in the alignment
process, it is impossible to correct this
later in the procedure.
– Arbitrary alignment.
Alignment of protein coding DNA sequences
• It is not very sensible to align the DNA
sequences of protein-coding genes.
ATGCTGTTAGGG
ATGCTCGTAGGG
ATGCT-GTTAGGG
ATGCTCGT-AGGG
The result might be highly-implausible and might not
reflect what is known about biological processes.
It is much more sensible to translate the sequences to
their corresponding amino acid sequences, align these
protein sequences and then put the gaps in the DNA
sequences according to where they are found in the
amino acid alignment.
Manual Alignment- software
GDE- The Genetic Data Environment (UNIX)
CINEMA- Java applet available from:
– http://www.biochem.ucl.ac.uk
Seqapp/Seqpup- Mac/PC/UNIX available from:
– http://iubio.bio.indiana.edu
SeAl for Macintosh, available from:
– http://evolve.zoo.ox.ac.uk/Se-Al/Se-Al.html
BioEdit for PC, available from:
– http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT
/bioedit.html