Tregwiki:Biopython-Meme example

import Bio.AlignAce.Motif as motif from Bio.Seq import Seq from Bio.Alphabet import IUPAC m = motif.Motif a = IUPAC.unambiguous_dna m.add_instance(Seq("ATATAT",a)) m.add_instance(Seq("ATATTT",a)) m.set_mask("******") print m.__str__

t = Seq("ATTATTATTATTATTATATATTT",a)

for o in m.search_instances(t): # search for exact matches print o

for o in m.search_pwm(t): # scan the whole sequence and score all positions print o

for o in m.search_pwm(t,0.5): # select only hits with score above 0.5 print o

(contributed by bartek wilczynski)