Writing a script to analyze similarity between 5 mitochondrial DNA sequences

Question

[jahanarahoque]

I have 5 mtDNAsequences of bird subspecies and I would like to convert them to mtRNA, I already have a script that could be used for that. I need someone to expand upon this script. I need to use some regular expressions to compute which mtrna sequence is closest to the one I am trying to compare it to. Then, I need to alter my closest sequence to find and replace the comparison sequence and print the results. I don't think it would take more than two hours to assemble the script.

Can anyone take a look at it today?

The sequences I'm looking at

https://drive.google.com/open?id=0B6mxnwYYXzZ0ZW03cGl0Q2VDZ2ZTZHFtbXl5R1l5NmFrcDU0https://docs.google.com/document/d/17wqdlIwUcy4eYNI9EG921aqailGuwiJ1ov2U7npo4Kk/edit?usp=sharing

#!/usr/bin/perl -w
# Transcribing DNA into RNA

# The mtDNA
$mtDNA = ;

# Print the mtDNA onto the screen
print "Here is the starting DNA:\n\n";

print "$mtDNA\n\n";

# Transcribe the mtDNA to mtRNA by substituting all T's with U's.
$mtRNA = $mtDNA;

$mtRNA =~ s/T/U/g;

# Print the mtRNA onto the screen
print "Here is the result of transcribing the mtDNA to mtRNA:\n\n";

print "$mtRNA\n";