Next: Tree of Minimum Gap
Up: Semi-automatic multiple alignment
Previous: Semi-automatic multiple alignment
Here semi-automatic multiple alignment method is proposed. The basic
idea is as follows:
- 1.
- Sequence data set is classified under certain criteria such as
sequence lengths and composition.
- 2.
- Multiple alignment is performed locally in each classified data
set.
- 3.
- The multiplly aligned data sets are joined sequentially. This
operation is performed by profile option of ClustalW [Thompson et al., 1994].
- 4.
- A guide tree is constructed.
- 5.
- Multiple alignment of whole data set is carried out following the
guide tree.
- 6.
- Steps 4 and 5 are iterated until no improvement is observed.
Programs make_gap_matrix and make_freq_matrix have been provided
for the step 1.
Satoshi OOta
1999-03-06