Thanks to Tim Littlejohn's kind help, I solved my problem with
trnascan. It really runs quite quickly (I searched about 800K of
data in less than 1/2 hour), or it runs infinitely if you forget
one important step. I got trnascan from the LANL mail server, and
it comes as one file in each mail message -- 2 C language files,
2 data files, and some documentation. Of course, to get the
thing to compile you have to strip the mail headers from the
C files, so I compiled it an started it running. and running.
Carefully reading the above account, you will notice that I forgot
to strip the mail headers from the two data files. Strip those
headers, and the program races through DNA. Don't strip the
headers, and it runs forever. A good object (or is it binary :-)
lesson for all us software developers.
Department of Cellular and Developmental Biology
Department of Genetics / HHMI
krobison at nucleus.harvard.edu