Re: Optimization algorithm help needed


Yes. A lot more information about your problem is needed.

No problem.

1. Is the sequence fixed? You want to design a set of "primers"
which is optimum for this sequence?

The sequence is fixed.

2. You've explained almost nothing about what a "primer"
does. I'm guessing that it is something that looks for
a specific sequence and snips the part between two
occurrences of that sequence.
a. Is that correct?

No. Primers are pairs of short DNA sequences which will amplify (make lots of) the sequence of DNA between them in PCR (explained below).
b. Is the number of primers fixed?

Yes. But not really relevant- I have a list of primers.

c. Is the length of the sequence a primer looks
for fixed?

Within a set range yes. But again not relevant, as I already have a list of primers.

d. What if there were n copies of that sequence?
Would the primer snip the whole strand into (n-1)
substrands at those points?

Nope.

3. What do you mean by coverage? If the effect of
P1 (for instance) in your drawing above is to snip
the sequence into 3 pieces, don't those 3 pieces
cover pretty much the whole strand?

P1 will amplify the region of the sequence between (and including) the >>>> and <<<<<.

4. What is PCR and what does "how well it works with
the PCR" mean?

Polymerase Chain Reaction. DNA is double stranded, with heat it separates. The primers bind to the single strands and then nucleotides (AGCT) are added on with cooling and enzymes. The heating/cooling cycle is repeated to produce lots of DNA from the primers used. Too complicated to explain more, check this out for more info:
http://en.wikipedia.org/wiki/PCR

But again, irrelevant. You have a list of PCR products (sequence flanked by primers) with scores and lengths. The trick is to cover your entire input sequence with these products in an optimal fashion based on score and length.

Hope this helps!
B
.

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