reading sequencing results - (May/02/2006 )

Hi,

When reading sequencing results, how do you decide to delete bases or even the rest of the sequence?

I get confused sometimes there is a peak that is sort of around and it says AAA and another peak which is more rounder and flatter and it says AAAA. I don't know how the programme decided it was 3 and 4 peaks. And I don't know how to correct it as I see just one flat around peak. I got some nice sharp peaks again after these.

I sent for sequencing of my insert within a plasmid backbone. Is it best to delete the plasmid backbone sequences out all togther before analysing the sequence result I have got? If so, why? If not, Why?

Thanks a lot in advance
Perl

Are these peaks around 80-120 bp into the sequence? If so, they are probably a dye blob artifact. If they are toward the 500-700 bp region, they are probably runs of multiple bases. The width of that peak will be the best key to the number of those bases. If you post the file, we can look more carefully.

It mostly comes from experience, but this is also why you must sequence the section multiple times in each direction (starting from different points along the way) in order to be certain of having the correct sequence...

Thanks a lot for the replies..

I started getting those flat peaks around 600bp into the sequence.

Any sugegstions to this question?
I sent for sequencing of my insert within a plasmid backbone. Is it best to delete the plasmid backbone sequences out all togther before analysing the sequence result I have got? If so, why? If not, Why?

Thanks so much again..
Perl