In article <8sl1d5$d4s$1 at news.net.uni-c.dk>, "S.W. Rasmussen" <swr at crc.dk> writes:
>Does anyone know of a simple DOS application which is able to extract the
>nucleotide sequence from ABI (310, 377, 3700) traces file without at the
>same time displaying the sequence plot? What I need is a program running
>under Windows (95/98/2000/NT) doing something like:
>> extract.exe infile=abifile1.plt outfile=abifile1.seq
>
Well, I don't have that, but there are some tools that can get you started
on that path, if you have a Fortran compiler and know how to program in that
language at:
http://seqaxp.bio.caltech.edu/pub/SOFTWARE/abitools.zip
here's what's in it:
ABITOOLS.ZIP
Tools and documentation for handling ABI files in a VMS
environment.
ABIBREAKOUT.FOR Fortran 77 program which converts an ABI trace file to
a text format. Read the comments at the top before using it.
ABIPRINTOUT.FOR,ABIPRINTOUT.CMD,ABIPRINTOUT.TXT,ABI_UTILS.FOR
Fortran 77 program which prints traces through
the GCG graphics interface after extracting
them from an ABI file. Can also use PHRED output
for better base calling.
EXAMPLE_ABIPRINTOUT.PS
One page of output from ABIPRINTOUT
PROCESS_ABI_FILES.COM
DCL procedure used at Caltech to batch
process ABI files, run them through PHRED,
and produce and print trace files for the
end users.
ABI.TXT Notes derived from binary spelunking in the
ABI files to figure out their organization.
DATASNIFFER.FOR Fortran 77 program that was used to figure out the
structure of ABI files. (Unlikely it
will work without modification on anything
other than a VMS machine.)
Use BINARY FTP to transfer
Regards,
David Mathog
mathog at seqaxp.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech
