Need some help find Open Reading frame in DNA using Regex?
I'm trying to find all the possible reading frames of a minimum nucleotide
length.
"A[TU]G(?:(...){3}){%d,}?(?:[TU]AG|[TU]AA|[TU]GA)" % (minimal_aa)
this pretty much does what I want, but for some reason, some reading
frames do not acknowledge some stop codons.
I'm sure it has something to do with the (...) portion. How do I tell it
to ALWAYS stop at [TU]AG|[TU]AA|[TU]GA, although passing through multiple
start codons is fine.
I'm using Python on Eclipse.
I'm using Pythex.org to check my strings, but here's a sample of what I'm
talking about:
AUGGAGAGCCUUGUUCUUGGUGUCAACGAGAAAACACACGUCCAACUCAGUUUGCCUGUCCUUCAGGUUAGAGACGUGCUAGUGCGUGGCUUCGGGGACUCUGUGGAAGAGGCCCUAUCGGAGGCACGUGAACACCUCAAAAAUGGCACUUGUGGUCUAGUAGAGCUGGAAAAAGGCGUACUGCCCCAGCUUGAACAGCCCUAUGUGUUCAUUAAACGUUCUGAUGCCUUAAGCACCAAUCACGGCCACAAGGUCGUUGAGCUGGUUGCAGAAAUGGACGGCAUUCAGUACGGUCGUAGCGGUAUAACACUGGGAGUACUCGUGCCACAUGUGGGCGAAACCCCAAUUGCAUACCGCAAUGUUCUUCUUCGUAAGAACGGUAAUAAGGGAGCCGGUGGUCAUAGCUAUGGCAUCGAUCUAAAGUCUUAUGACUUAGGUGACGAGCUUGGCACUGAUCCCAUUGAAGAUUAUGAACAAAACUGGAACACUAAGCAUGGCAGUGGUGCACUCCGUGAACUCACUCGUGAGCUCAAUGGAGGUGCAGUCACUCGCUAUGUCGACAACAAUUUCUGUGGCCCAGAUGGGUACCCUCUUGAUUGCAUCAAAGAUUUUCUCGCACGCGCGGGCAAGUCAAUGUGCACUCUUUCCGAACAACUUGAUUACAUCGAGUCGAAGAGAGGUGUCUACUGCUGCCGUGACCAUGAGCAUGAAAUUGCCUGGUUCACUGAGCGCUCUGAUAAGAGCUACGAGCACCAGACACCCUUCGAAAUUAAGAGUGCCAAGAAAUUUGACACUUUCAAAGGGGAAUGCCCAAAGUUUGUGUUUCCUCUUAACUCAAAAGUCAAAGUCAUUCAACCACGUGUUGAAAAGAAAAAGACUGAGGGUUUCAUGGGGCGUAUACGCUCUGUGUACCCUGUUGCAUCUCCACAGGAGUGUAACAAUAUGCACUUGUCUACCUUGAUGAAAUGUAAUCAUUGCGAUGAAGUUUCA
UGGCAGACGUGCGACUUUCUGAAAGCCACUUGUGAACAUUGUGGCACUGAAAAUUUAGUUAUUGAAGGACCUACUACAUGUGGGUACCUACCUACUAAUGCUGUAGUGAAAAUGCCAUGUCCUGCCUGUCAAGACCCAGAGAUUGGACCUGAGCAUAGUGUUGCAGAUUAUCACAACCACUCAAACAUUGAAACUCGACUCCGCAAGGGAGGUAGGACUAGAUGUUUUGGAGGCUGUGUGUUUGCCUAUGUUGGCUGCUAUAAUAAGCGUGCCUACUGGGUUCCUCGUGCUAGUGCUGAUAUUGGCUCAGGCCAUACUGGCAUUAA
wait. this is a bad example. because it actually checks out right now that
I eyeball the output. I had to shorten this, but there was one code a few
thousands of nucleotides that was riddled with stop codons and nothing was
working properly. I hope you get what I mean, if not don't worry.
Thanks in advance amigos!
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