The program ``sortsco'' allows the sequence fragments that are aligned to the query to be output. It also permits the fragments to be extended to the N and C terminii by a predefined percentage. The program also allows the top N hits to be output, or all those that score above a cutoff. Further analysis tools are under development. Just type ``sortsco'' to see the program options.
sortsco will also read a file of ID codes to allow these sequences or just the titles to be extracted from the database. The program will read the output of the standard scanps scan (ie not using the NALL method) and sort the results if you do not want to use the Unix sort utility. Normally sortsco is a little slower at the sort than Unix.