[BiO BB] database for genome...

hz5 at njit.edu hz5 at njit.edu
Sat Sep 7 20:15:21 EDT 2002

My professor tell me suffix tree is really helpful!

Quoting Tarak Upadhyaya <hyndu007 at hotmail.com>:

> I have the genome on my harddrive, and I'm trying to find ways to put it
> in 
> a data structure/database so I can access it faster, or scan through it
> faster. Currently it takes my cpu 128 seconds to go though chromosome 1.
> The 
> way I coded it, however, seems like there is room for optimization.
> While I 
> do that I also want to think of a way to put it in a database so i can
> add 
> more functionality/speed. Maybe something like a quadratic tree? [binary
> tree, but each node branches out into 4 seperate nodes, representing the
> nucliotide bases].
> -Tarak Upadhyaya
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Haibo Zhang
Computational Biology, NJIT & Rutgers University

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