[Biodevelopers] Re: [BiO BB] database for genome...

[Joe Landman]

Hi Tarak:

  A few points.  First, we have a nice biodevelopers group that has many
people who might be able to help with this.  Second, from a program
performance point of view, what is your code doing?  Are you simply
looking at how long it takes to read in the chromosome, or are you doing
processing in the loop as well?  Is the data in a flat file (somewhat
implied)?  A database will not speed up read access unless you need to
look at small specific subsets of the data.

  Before building other data structures, a better understanding of what
the code is doing, how it is doing it, and so forth are in order. 
Please describe it in greater detail, and post it to biodevelopers.

Joe


On Sun, 2002-07-21 at 14:25, Tarak Upadhyaya wrote:
> 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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-- 
Joe Landman,
email: landman at scientificappliance.com
web  : http://scientificappliance.com