gcgtmp 3% ls
cdk2-psq.fasta		cdk2.txt
gcgtmp 4% fromfasta

FromFastA reformats one or more sequences from FastA format into
single sequence files in GCG format.

 FROMFASTA of what FastA sequence file(s) ?  cdk2-psq.fasta

 gi-251620.pep  298 aa.
 gi-666951.pep  298 aa.
 gi-1754601.pep  106 aa.
 gi-312803.pep  298 aa.

 Finished FROMFASTA with 4 files written.
 1000 sequence characters were reformatted.
gcgtmp 5% ls
cdk2-psq.fasta  gi-1754601.pep  gi-312803.pep
cdk2.txt        gi-251620.pep   gi-666951.pep
gcgtmp 6% chopup cdk2.txt

ChopUp converts a non-GCG sequence file containing lines longer than 511
characters and as long as 32,000 characters into a new file containing lines no
longer than 50 characters.  The new file can be read by Reformat to create a
GCG-format sequence file.

 What should I call the chopped file (* cdk2.dat *) ?


 All of "cdk2.txt" chopped up without error!

gcgtmp 7% reformat cdk2.dat

Reformat rewrites sequence file(s), scoring matrix file(s), or enzyme
data file(s) so that they can be read by GCG programs.
 No ".." divider
        cdk2.dat  length: 298 aa
gcgtmp 8% gcgtoblast

GCGToBLAST combines any set of GCG sequences into a database that you can
search with BLAST.

 GCGTOBLAST of what input sequence(s) ?  *.pep

 What should I call the database ?  cdk2psq

           GI-1754601     106 characters.
            GI-251620     298 characters.
            GI-312803     298 characters.
            GI-666951     298 characters.

 GCGTOBLAST complete:

            Sequences: 4
              Symbols: 1,000
      Output files in: .

gcgtmp 9% blast -BAT -IN2=cdk2psq

BLAST searches one or more nucleic acid or protein databases
for sequences similar to one or more query sequences of any
type. BLAST can produce gapped alignments for the matches it
finds.

 Blast with what query sequence(s) ? cdk2.dat

                  Begin (* 1 *) ?
                End (*   298 *) ?

 Ignore hits expected to occur by chance more than (* 10.0 *) times?

 Limit the number of sequences in my output to (* 500 *) ?

 What should I call the output file (* cdk2.blastp *) ?

 ** blast will run as a batch or at job.

 ** blast was submitted using the command:
    "  at now  "

       warning: commands will be executed using /bin/sh
job 1016726378.a at Thu Mar 21 23:59:38 2002
gcgtmp 10% cat cdk2.blastp