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From "Bruno P. Kinoshita" <brunodepau...@yahoo.com.br.INVALID>
Subject Re: TEXT-77 | String palindrome API
Date Thu, 22 Jun 2017 04:28:21 GMT
Palindromes (and other algorithms like De Bruijn graphs, lcs) are normally taught in most introductory
bioinformatics courses. Not sure how much palindromes are used though. I know use cases for
De Bruijn and lcs.

Maybe taking a look at BioJava could help - https://github.com/biojava/biojava-legacy/blob/a909c76131400e6f60048566e33a03f45da2f492/core/src/main/java/org/biojava/bio/molbio/RestrictionEnzyme.java#L291


Palindromes in bioinformatics are not normally used as in text processing. If we had tokenizers,
then I think maybe we could identify palindromes in words, in sentences, and in proteins,
though not entirely sure.

But would be good to find someone, maybe a bioinformatician, that could confirm if it would
be useful, and give a few use cases, for that.

Cheers

Bruno

ps: BioJava is an interesting project, that could maybe someday use [text]. They already use
[dbcp], [cli] (transitive from jmol I think), and [math]

________________________________
From: Amey Jadiye <ameyjadiye@gmail.com>
To: Commons Developers List <dev@commons.apache.org> 
Sent: Thursday, 22 June 2017 3:51 PM
Subject: Re: TEXT-77 | String palindrome API



Hi,

With little research I found[1] we do have use cases for it like in biology
(I think Bruno might be referring the same fields for its application)

"Palindrome recognition is important in computational biology. Palindromic
structures can frequently be found in proteins and identifying them gives
researchers hints about the structure of nucleic acids. For example, in
nucleic acid secondary structure prediction, one is interested in
complementary palindromes which are considered in the full version."


[1]http://drops.dagstuhl.de/opus/volltexte/2014/4454/pdf/12.pdf

Regards,
Amey


On Jun 22, 2017 12:42 AM, "Emmanuel Bourg" <ebourg@apache.org> wrote:

> Le 21/06/2017 à 19:17, Amey Jadiye a écrit :
>
> > Though its very trivial to build, by any chance we should have palindrome
> > method in Apache Commons API ? there is nothing bad having this tool in
> > our arsenal, preferably in StringUtils ?
>
> Like sebb I fail to see the use case for this. Checking palindromes
> looks more like an academic exercise to me than a useful feature of a
> text oriented library.
>
> Emmanuel Bourg
>
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