Re: [MLUG] String manipulation in C

[Mike Miller <EMAIL:PROTECTED>]

On Sun, 1 Jul 2007, Jack Smith wrote:

> You hit the nail right on the head with what I need to do, Dr. Smith. My 
> project is doing gene sequence to DNA probe mapping. I have a file with 
> 600k lines of 5-50 base-pair (letter) probes and I need to see if there 
> are sequences that are identical to the probes' sequences in the DNA 
> sequences. The chromosomal DNA sequence fragments are roughly 500-1500 
> bp long and there are about 29k of them. I need to see any and all 
> matches between the probes and the chromosomal DNA as well as where in 
> that DNA sequence the match occurs. In short, I want something like 
> this:
>
> Probename  Sequence    Gene name   Match Start BP   Match End BP
> Probe1     AAGGCC      Gene1       50               55
> Probe1     AAGGCC      Gene1       95               100
> Probe2     CCGACGT     Gene1
> Probe3     [AG]CCT     Gene1       65               68

So the big job is essentially grepping 600,000 times through a file of 
29,000 lines.  That will probably never be all that fast of a job, but if 
you only need to do it once and you can dedicate a computer to it, you'll 
be done faster if you don't spend a lot of time on optimizing the code.

Mike

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