Better analysis of automated sequencers?

Johan deBoer jdboer at SOL.UVIC.CA
Thu Aug 12 00:43:54 EST 1993


We have a couple of Pharmacia ALF sequencers and ABI sequencers. We use them
to sequence the same gene over and over again to find mutations (different
mutants of same sequence). The gene is about 1000 bp long, so several 
primers are usually needed. The resulting sequences that the machines
produce are then lined up together with the wild type sequence using 
DNA-STAR, and any non matching positions are possible mutations.

Not all of these are mutations of course, since there are always ambiguities.
The software for all this, the base calling routines of the machines, and the
alignment with wild type sequence and overlappings are really geared to use
with new sequences. I have a feeling that there must be a better way of doing
these base callings, and comparisons in cases where the wild type sequence
is already known, and all we want is compare the machine output with this
to find the single change.

Is there someone out there who has ideas about this, or perhaps using a
different system to do this? Your comments would be greatly appreciated.

Johan de Boer
jdboer at

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