Beefy Boxes and Bandwidth Generously Provided by pair Networks
Your skill will accomplish
what the force of many cannot

Re: Multidimensional regular expressions

by MadraghRua (Vicar)
on Nov 19, 2002 at 22:00 UTC ( #214282=note: print w/replies, xml ) Need Help??

in reply to Multidimensional regular expressions

It strikes me that something like this has already been encountered in bioinformatics. Try out Algorithms on Strings, Trees and Sequences by Dan Gusfield or Computational Molecular Biology by Pavel Pezner.

So in bioinforamtics, an individual sequence can be considered an array. Comparing a pair of sequences can be like comparing an array with an array. The dimensionality increases with the number of sequences that you want to compare. Typically a two dimesional comparrison is carried out n-1 times on the data set to perform an initial comparison, resulting in a statistical score. You then pop the initial query sequence from the data set and carry through the comparrison with the remaining sequences until you have only one left in the set. The statistical score is used to sort the results in terms of relatedness.

This might then be represented as a tree of sequences with branches and proximity indicating closeness of similarity, or a multiple sequence alignment where the distance of two sequences from each other in the alignment indicates their degree of similarity. You might look into a program called ClustalW for some examples of how this is done.

I hope this adds some fuel to your fire.

yet another biologist hacking perl....

  • Comment on Re: Multidimensional regular expressions

Log In?

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://214282]
[Your Mother]: The US government does not attract talent, but grafters and liars and it has been that way for the better part of a century. FEW exceptions.
[erix]: you think it only /looks/ worse this time?
[Your Mother]: HR Clinton was literally threatening Russia. She would have been MUCH more likely to start real trouble.
[Your Mother]: I think there is less decorum this time.
[Your Mother]: We’ve had rapists and thieves and unqualified government. They just had decorum.
[erix]: heh, understatement of the week :)
[erix]: well, I hope you're right
[Your Mother]: Bill Clinton assaulted and raped repeatedly. Even when it was hinted and finally all but proved, no one cared because his sexism, and racism, and killing was decorous.
[Your Mother]: I think Trump might be better specifically because no one respects him so he won't get his way the way the others did.
[Your Mother]: (I certainly did not vote for him and have been an outspoken critic of his for three decades, by the by.)

How do I use this? | Other CB clients
Other Users?
Others lurking in the Monastery: (8)
As of 2017-01-20 01:01 GMT
Find Nodes?
    Voting Booth?
    Do you watch meteor showers?

    Results (173 votes). Check out past polls.