About DNA sequencing

Jose de las Heras via methods%40net.bio.net (by josenet from tiscali.co.uk)
Sun Oct 7 13:56:08 EST 2007

"kou" <koustubhvaze2 from googlemail.com> wrote in message 
news:1191777162.303207.112430 from 50g2000hsm.googlegroups.com...
> Hello everybody,
> I am PhD stdent and working on circadian rhythms in Drsophila.
> I am planning to do sequencing of period locus for detecting
> polymorphism.
> I have a very basic question about sequencing :
> After sequencing, entire sequence is not accurate. stretch of sequence
> immediately after primers is not accurate.
> So my question is
> How to choose accurate sequence ?
> I mean what should be the start  point and end point  of accurate
> sequence with respect to primer position?
> Kou

With the sequence you will also get the "traces". This is a graph showing 
the peaks for each of the four nucleotides (the files frobably have 
extension "ab1", although there are other formats). This graph allows you to 
decide how "nice" your sequence is. If you want to be sure of your sequence 
you should repeat the sequencing, if possible also including sequencing the 
other strand.
Ask somebody in your lab who deals with sequences, they should be able to 
show you what the traces look like. You may already have access to a good 
commercial program to sort DNA sequences, but if not, I find the free 
software BioEdit very useful (google).
Ask what people in your lab use and they should be able to show you.

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