In article <9303292333.AA19018 at molly.sdsc.edu> romberg%molly at SDSC.EDU (Lori Romberg) writes:
>>I am using Fasta to run DNA as well as protein searches against a
>database of sequences. By default, the sequences are sorted and
>outputed by their initn scores. There is a command line option to
>sort by the init1 scores, but I can't find an option to sort by the
>optimized scores which is what I need to do for my purposes.
>>Does anyone know of an easy way to do sort by the optimized scores
>without actually going into the source code? Any help would be
Use the -o option. This will slow a protein search about 2X,
because optimized scores are calculated for many more sequences. It
also improves senstivity substantially. I do not think that it is
worthwhile for DNA sequences.