[Biopython] Motif search problem

[Eric Ma]

Hi everybody,

We're having some problems doing a motif search.

We'd like to search a set of 2000 amino acid sequences for a set of motifs.
The motif set is A{P}NL, where {P} means "any amino acid but proline".
We're trying to avoid manually creating every Seq() object containing every
combination.

We have tried AXNL, but that searches for any "AXNL" (literally) in the
sequence, not a degenerate amino acid sequence.

Sample code looks like the following:

instances = [Seq("ANNL", IUPAC.extended_protein)] #<-- this is the line
which is troublesome
m = motifs.create(instances)
#sequences is a list of lists, where each sublist looks like
['Accession(String)', 'Seq() Object']
for record in sequences:
    for pos, seq in m.instances.search(record[1]):
        print record[0], pos, seq

Does anybody have suggestions as to how we can go about modifying the
"instances" line so that we don't have to type in every single combination?

Cheers,
Eric
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