Using PERL to solve a specific bioinformatics problem

M

michaelzhao

Hi, I am an undergraduate research student at Georgia Institute of
Technology. My undergraduate research field falls into bioinformatics.
My professor recently charged me with solving a bioinformatics problem
as a learning process using PERL. I am free to use any and all
resources to solve it. I have never programmed at all before and
learning PERL using the book "Beginning Perl for Bioinformatics" by O
'Reilly.

I have a set of 30 nucleotides upstream of verified E. coli genes. The
task is to find an efficient way to generate Markov chain transition
matrices for sequences of arbitrary length. Zero, first, and second
order should be sufficient. Also, I need a way to score sequences
against those transition matrices.

I am asking for any helpful tips and hints I should go about doing
this. As this is my first problem I am in the dark a little bit with
no real idea of where to start. Any and all help is appreciated.
Thanks!

~Michael
 

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