>How do the alignment algorithms/strategies of CLUSTALW relate to the
>algorithms used in say BLAST or tools similar to BLAST ? Is there any reason
>to prefer one over the other ?
As far as I am aware they both use a local alignment strategy . Blast is
aprogram used more for scanning large databases looking for sequences
similarity where clustalw is a program more often used for Multiple sequence
alignment and Identifying homology( eclustalw is way better than gcg's Pileup)
>Would someone have any comments on the differences between the PAM and
>BLOSUM distance arrays, particularly with regard to their logic, derivation,
>application and relative accuracies.
The major difference between the PAM/MDM/DAYHOFF matrices are that these are
derived from global alignments of closely related sequences while the BLOSUM
series are erived from local, ungapped alignments of distantly related
sequences. For this reason you can see that the Blosum serires perform better
for local similarity searches.
Hope this helps
Nadia Anwar