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Re: how to find this substring?

by ckj (Chaplain)
on Jun 08, 2012 at 12:24 UTC ( #975154=note: print w/ replies, xml ) Need Help??


in reply to how to find this substring?

Assuming $seq as the string provided by you. Try this:

$seq='GTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGG..........GGAGTT'; $a = 'ATG'; $b = '(TAA|TAG|TGA)'; while($seq =~ /($a(.*?)$b)/g) { print $1."\n\n\n"; }


Comment on Re: how to find this substring?
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Re^2: how to find this substring?
by Not_a_Number (Parson) on Jun 08, 2012 at 14:08 UTC

    From the OP:

    I need to read some DNA sequences and check if they start with 'ATG' and end in 'TAA', 'TAG' or 'TGA'

    Given the sequence:

    ATGXXXTAAXXXTAA

    your code outputs:

    ATGXXXTAA

    whereas it should print the whole string (or 'true', or whatever).

      (o.O)

      So, why can't you change line 6 to be print "whatever\n\n";?

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