#3 Reference Sequence as template

[Ido M. Tamir]

Hi,
currently it is possible to specify a reference trace in
pregap4 for mutation detection.
It is also possible to specify a sequence, but this is only
used for reporting the position of mutations and is
optional.

Would it be possible to use only the reference sequence
as a reference or backbone of a contig to which all
traces are aligned?

[James Bonfield]

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It is possible to assemble a large text sequence into a gap4
database in the same manner that you assemble other
sequences. If you put this at the start of your file of
filenames then it will be assembled first (assuming you do
not use one of the external assembly tools, such as phrap,
cap or fakii). A sequence does not need to be labelled as
"reference sequence" for it to be assembled and compared
against.

The only thing that this doesn't do is to force all traces
to be compared against your reference sequence, so it's
possible that some traces may get assembled into their own
contigs if they differ too much.

Does this address the request sufficiently?

James