gp_tm - calculate stem/loop and dimere structures of an oligonucleotide
gp_tm [-m] [-q] [-v] [-d] [-h] [inputfile] [outputfile]
- for each sequence, prints the sequence number, the dG values for the
most stable dimere and the most stable stem/loop, and the sequence name, all
fields separated by a TAB.
- -m value
- sets the maximal number of structures to be shown (default 5)
- Prints the version information.
- Prints lots of debugging information.
- Shows usage information.
- file to proces; if not given, will use standard input
- file to write the data to; if not given, will
use standard output
All Genpak programs complain in situations you would also complain,
like when they cannot find a sequence you gave them or the sequence is not
The Genpak programs do not write over existing files. I have found this
feature very useful :-)
I'm sure there are plenty left, so please mail me if you find them. I tried
to clean up every bug I could find.
January Weiner III