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Re: Finding biological palindromes

by igelkott (Priest)
on May 08, 2014 at 21:08 UTC ( [id://1085508] : note . print w/replies, xml ) Need Help??

in reply to Finding biological palindromes

Perhaps you already know this but DNA palindrome is a fairly casual way of saying inverted repeat. Not trying to be picky but the latter term should help with the search.

With this in mind, BioPerl has an interface to the relevant function of the popular (and huge) EMBOSS package.

Possibly a bit too narrow but you might also want to take a look at a recent paper which uses a Perl script to find a particular type of inverted repeat (MITE).

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Re^2: Finding biological palindromes
by TJCooper (Beadle) on May 12, 2014 at 09:42 UTC
    Many apologies for the delay in replying to this thread. As per the advice above i've decided to make use of existing biological tools (EMBOSS) and wrapping this in bioPerl to get a suitable output format rather than constructing something from scratch. I will post the solution when it's completed and also explain it for non-biologists to answer the questions below. Thanks again!