in ~cmungall/data you will find a 
directory called new-ests/

in this directory there are various EST sequences
in individual fasta files. some of these are 3 prime
some are 5 rpime

using only unix pipes, the unix grep command and the
two programs in ~cmungall/data  try and make a combined
fasta file containing only 5 prime sequences

you should be able to do this in one step.

hint:

the program fasta2flat.pl can be used to convert fasta to
a flattened format containing one line per sequence, and
flat2fasta.pl can be used to convert back to fasta