Sat Nov 27 11:11:58 PST 2004 Kevin Karplus

The monthly update of the database takes too long, mainly because
modest hits trigger recomputation, even if there are much better hits
already in the template library for the target protein.  I need to
come up with a better way of filtering to select recent.ids.



Sat Nov 27 11:13:37 PST 2004 Kevin Karplus

The scripts and Makefile need to be redone to do the sam-t04 method,
rather than the sam-t02 method.


Sat Nov 27 11:14:34 PST 2004 Kevin Karplus

There should be an annual update to redo the multiple alignments, at
least for proteins with relatively few homologs or no good structure
predictions.  The monthly update only redoes the searches, not the
multiple alignments.


Sat Nov 27 12:27:57 PST 2004 Kevin Karplus

The multi-level recursive make for creating the alignments turns out
to be very slow---the make takes forever to decide that all the needed
alignments are done.  I need to come up with an efficient way to
create lots of alignments as needed, without needing a complicated script.
What I *really* need is something like "make" but that allows multiple
variables in the file name.

This is particularly a problem for targets with many good hits, like
YJL130C, which has 346 templates, and takes days to check all the alignments.
Perhaps we should limit the number of templates to 100?