Find and Mark TATA Box

hannsschweis
hannsschweis used Ask the Experts™
on
Hi Guys,

Can you help me with finding and marking TATA Box and identifying Open Reading Frames(ORFs) by marking start codon(methionine only) and stop-codon. I am trying to do it in perl language....

thanks in advance
Comment
Watch Question

Do more with

Expert Office
EXPERT OFFICE® is a registered trademark of EXPERTS EXCHANGE®

Commented:
Can you give us some example data?

Author

Commented:
Input:

GAATTCCATATCTTTGCCAAACACTTGGTGTTTCCACCCTTTTTAATTTTAGCCTTTCTGCTAGGTGTATAGTGGTTTCTCATTGTGATTTTATTTCTCTAAAGACTAGTGATGATTCATTTTAATATAATAATAAGTTAGAATAGATGTATTGGGATTCTGTAGATCAATTCGGGGAGGATGATAAGAATATTGAATCCTGCAATCGATGAATACACAAAGCTTTCCTAGGAAATATTTGCCTTTATTCACTCACATATTTTCTTTCCTTCTGGGCATAATAAGAGGAACTTAGGGAAAACAGGCCTTGGTTCTGCATTCTCAGTAAAGGCCTTGATCTCTCTCTTTAATTTTCATGCATGATCTTTCCTCTCTATTTCTTTTCTTTCCTCTCTCTTTTCTCCTTCTCCCATTTCCTGGTAAAGATAGTTGATTGCACAGAGTCTGGAATCCTCTGTGAGTAGGTTCACATTCCAATTCTTCAACTTACTTATTTCTGATGGACAGGGATTTACTTTTTCATCTTATTTTGAGTTTCTATTTATTTTACTTTTTTATGACAAATTTTTTTTTTTTTTGAGACAGGCAAATCGGCATAACCGCCCT
If start codon is ATG and end codon is one of TAA, TAG, or TGA and if you want to fold the data at an ORF:

#!/usr/local/bin/perl

my $orf = <DATA>;
my $strtcodon = "ATG";
my $endcodon = "TAA|TAG|TGA";


$orf =~ s/($strtcodon.*?TATA.*?(?:$endcodon))/\n$1\n/gi;
print $orf;

__DATA__
GAATTCCATATCTTTGCCAAACACTTGGTGTTTCCACCCTTTTTAATTTTAGCCTTTCTGCTAGGTGTATAGTGGTTTCTCATTGTGATTTTATTTCTCTAAAGACTAGTGATGATTCATTTTAATATAATAATAAGTTAGAATAGATGTATTGGGATTCTGTAGATCAATTCGGGGAGGATGATAAGAATATTGAATCCTGCAATCGATGAATACACAAAGCTTTCCTAGGAAATATTTGCCTTTATTCACTCACATATTTTCTTTCCTTCTGGGCATAATAAGAGGAACTTAGGGAAAACAGGCCTTGGTTCTGCATTCTCAGTAAAGGCCTTGATCTCTCTCTTTAATTTTCATGCATGATCTTTCCTCTCTATTTCTTTTCTTTCCTCTCTCTTTTCTCCTTCTCCCATTTCCTGGTAAAGATAGTTGATTGCACAGAGTCTGGAATCCTCTGTGAGTAGGTTCACATTCCAATTCTTCAACTTACTTATTTCTGATGGACAGGGATTTACTTTTTCATCTTATTTTGAGTTTCTATTTATTTTACTTTTTTATGACAAATTTTTTTTTTTTTTGAGACAGGCAAATCGGCATAACCGCCCT
Suhas .Senior QA Manager

Commented:
This question has been classified as abandoned and is closed as part of the Cleanup Program. See the recommendation for more details.

Do more with

Expert Office
Submit tech questions to Ask the Experts™ at any time to receive solutions, advice, and new ideas from leading industry professionals.

Start 7-Day Free Trial