Standard Chromatogram Format info?

James Bonfield jkb at mrc-lmb.cam.ac.uk
Mon Apr 21 04:31:54 EST 1997


In article <E8uvwE.IHM at ecf.toronto.edu> yuwaraj at ecf.toronto.edu (Murugathas Yuwaraj) writes:
>
>Greetings everyone!
>
>I am looking for information on the 'Standard Chromatogram Format'.
>Could someone kindly point me to some sources? I am interested in
>converting ALF data files (obtained from the Pharmacia sequencers)
>to SCF. I would also like to convert non-standard file formats (in
>the future) to SCF.

The full SCF spec is available on our ftp site. There's a link from the
http://www.mrc-lmb.cam.ac.uk/pubseq/formats.html page.

Note that the Version 3.00 format stores identical information to the
Version 2.02 format, but in a different order. The reasoning for this
was to aid compression. Compression itself is not part of the SCF
spec, but something which can be simply applied before reading or
writing files. The version 3 files (converted as 8 bit sample data
from ALF files) compress with bzip down to about 20% of their original
size (10% of the ALF sizes).

Modern ALF software outputs SCF version 3 files as standard. Infact as
far as we're aware now only ABI have their own format.

We have code for handling SCF files freely available. See
ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/src/. It's called
"io_lib". However we need to update the ftp site with newer code. We
also have code that reads both the ALF and ABI formats, but do not
distribute this as part of io_lib as we don't know the legal
implications.

	James
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/




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