The directory, Sequence-2-Sequence, contains a program to do alignments between two or more sequences by dynamic programming.
The directory, Sequence-2-Structure, contains a program to do a single alignment between a protein sequence and a protein structure by dynamic programming. This process of predicting a protein structure for a sequence is called "threading".
Because it was long ago, I do not remember much of my involvment with this project. From some of the Perl scripts that I wrote, it has something to do with optimizing certain parameters for aligning two protein structures. I would have to review these files again to get a better understanding.
The Perl scripts in following directories in the main LOOPP directory are my contributions:
ktd0_opt
x2xoptpmtest
Some results of this optimization procedure are in the log files in the following directory:
x2xvss2s