[EMBOSS] question about 'fuzznuc'and 'urzpro'

[Jean Mao]

Hi,

I know I can give a pattern like 'ACCGGT' and search against a file which
contains multiple sequences. Is there a way I can specify a 'pattern file'
which contains multiple patterns that I want to search for instead of just
one pattern each time? For example, I have a fileA which contains multiple
DNA sequences. I want to create a fileB which contains 20 patterns that I
want to seach each of them against the sequences in the fileA. We are in the
transition from GCG to EMBOSS. And the program 'findpatterns' in GCG can do
this. But I couldn't find corresponding emboss program that does the same
thing.

Thank you in advance.

Jean Mao
Helix Staff
CIT, NIH