ABI trace files

David Mathog mathog at seqaxp.bio.caltech.edu
Thu Oct 19 11:13:20 EST 2000


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 







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