missing nucleotide close to the primer

Wolfgang Schechinger marsupilamiwolfgang at web.de
Thu Feb 14 08:46:42 EST 2002

Dear Frank annd N., 

In my experince sometimes there are peaks in the beginning chromatogram that are irritating the base calling software. Probably originating from not so good seqencing Rxn or incomplete cleanup.

I got used to always checking the data against the chromatogram, conveniently done by BLASTing the data file against the expected sequence and then checking the differing regions.


Frank at Fackelmayer.de schrieb am 13.02.02:
> nsalazar at hgmp.mrc.ac.uk wrote:
> > 
> > Hi there,
> > Is it possible to miss a nucleotide in a stretch of about 60 nucleotides close to the
> > primer that was used for the sequencing reaction ?? I got a nucleotide deleted
> > (missing) from two different DNA sequences...
> > 
> In case you did check the original gel/chromatogram, and you are
> experienced in doing so: No, I don´t feel that the sequencing misses
> bases. To be on the safe side, use a different primer and/or sequence
> the other strand.
> Frank

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