update on seqpup and SCF file reading
Thu Jul 10 14:05:38 EST 1997
A few weeks back I replied to a query from Suzanne McNeely
who was looking for an SCF file reader. She had tried the
free program SeqPup that I author, without success. I realized
later that the way one reads SCF/ABI files with SeqPup isn't as
simple and well documented as it could be. It is still a preliminary
part of this program, and hasn't had the details worked out.
One can't use the File/Open sequence... command in SeqPup
to open SCF files. It uses a child application, specifically
Reece Hart's (Wash U bioinformatics) Autoseq program to translate
SCF and some ABI format trace files into base-called sequence files.
Look for the autoseq entry under childapps. You need to first
choose the file you want from the AutoSeq Base calling dialog,
then hit the Launch App button to do the calling and conversion
to files that SeqPup the main program can read. If the Autoseq
program successfully converts the trace file, it will create a
file xxxx.tfs which then should be automatically loaded into
SeqPup where you will see the traces for the bases in color and
can then edit (to some extent) the auto calling of the bases,
and can copy the sequence into a regular sequence file.
This part of SeqPup was still very preliminary in its operation,
and I haven't had time to go back to it and smooth out its
There is an MS WIndows version for this as well as Mac version.
There is a sample set of files that come with the seqpup
distribution for autoseq analysis. Try the autoseq.data/ files
to see if you can get them working. The files autoseq.data/ba16d1.s1
and autoseq.data/ba16d4.s1 are ABI format files.
u--bloomington--gilbertd at bio.indiana.edu
More information about the Autoseq