the forward and reverse strand of my nucleotide sequence do not complement exactly, there are few mismatched or additional base here and there. help

shinysangma said:

"my nucleotide sequence"

could you clarify what sequence you are talking about, where it came from and what help you want?

i got my 500bp pcr product(plant DNA) sequenced. The nucleotide sequence given by forward primer do not complement exactly the one given by reverse primer, especially towards the extremities(i.e, 3' & 5'ends). i have subjected the sequence of reverse primer to 'EMBOSSrevseq' before checking for complementary alignment. how can i edit my nucleotide sequencing result.
thaks

If you want to edit the sequence manually, perhaps you could use one of these tools?

http://gentle.magnusmanske.de/
http://www.bioinformatics.org/annhyb/

I found those links at the Open Science Project

You may also find useful software in the

Bioinformatics Links directory - DNA section

shinysangma said:

i got my 500bp pcr product(plant DNA) sequenced. The nucleotide sequence given by forward primer do not complement exactly the one given by reverse primer, especially towards the extremities(i.e, 3' & 5'ends). i have subjected the sequence of reverse primer to 'EMBOSSrevseq' before checking for complementary alignment. how can i edit my nucleotide sequencing result. thaks

It sounds like you are just seeing some sequencing errors. Did you only get a single read from each primer for this amplicon?

thanks. yes i got a single read for each primer. the sevice company gave me the electrophorogram and the nucleotide sequence(in notepad). yes, i am talking about the sequencing errors that i am unable to resolve.

shinysangma said:

thanks. yes i got a single read for each primer. the sevice company gave me the electrophorogram and the nucleotide sequence(in notepad). yes, i am talking about the sequencing errors that i am unable to resolve.

With only two reads it might be difficult to resolve which is correct. You should be able to compare the quality score at the positions that disagree. The one with the better score is likely the way to go.