Editview alternative

Sven Klages klages at molgen.mpg.de
Fri Sep 1 08:24:52 EST 2000


Dear James,
I checked some SCF files from Beckmann's Ceq2000 from September
1999.
Since we were just testing the machine I just have a few files.
But scf_dump gave me something like this ...
The significant difference seems to be the version (2.10 -> 3.00)
and of course the "[bases]" block.
Did I misunderstand the SCF definition in the Staden Manual ??
It's possible to read those files with progs like 'chromas'.

[Header]
779314022       # magic_number
20001           # samples
7064            # samples_offset
578             # bases
0               # bases_left_clip
0               # bases_right_clip
128             # bases_offset
0               # comments_size
0               # comments_offset
3.00            # version
2               # sample_size
2               # code_set
171618          # private_size
167072          # private_offset
0               # spare[0]
0               # spare[1]
0               # spare[2]
0               # spare[3]
0               # spare[4]
0               # spare[5]
0               # spare[6]
0               # spare[7]
0               # spare[8]
0               # spare[9]
0               # spare[10]
0               # spare[11]
0               # spare[12]
0               # spare[13]
0               # spare[14]
0               # spare[15]
0               # spare[16]
0               # spare[17]

[Bases]
C 00069 004 249 000 000   000 000 000  #  0
T 00081 000 000 000 250   000 000 000  #  1
T 00103 000 000 000 248   000 000 000  #  2
G 00118 000 000 253 000   000 000 000  #  3
A 00144 216 000 010 000   000 000 000  #  4
C 00154 000 243 000 000   000 000 000  #  5
A 00168 217 000 000 015   000 000 000  #  6
T 00188 000 000 000 253   000 000 000  #  7
G 00216 000 000 253 000   000 000 000  #  8
C 00242 000 253 000 000   000 000 000  #  9
C 00267 000 247 004 000   000 000 000  # 10
T 00279 000 000 000 250   000 000 000  # 11
G 00304 000 001 252 000   000 000 000  # 12
C 00331 000 253 000 000   000 000 000  # 13
[...]



Well, but that doesn't answer the original question, if there's
a Mac Software which is able to read SCF file ...
Sorry Perry, there's lots of software for win or Unix systems,
I just don't know any other Mac software than SeqA3.x or EditView.

best regards

Sven Klages

MPI f=FCr Molekulare Genetik
Ihnestra=DFe 63/73
14195 Berlin
** Germany **

** the first posting went accidentally wrong ... **


James Bonfield schrieb:
>=20
> In <8nsevv$i7o$1 at mercury.hgmp.mrc.ac.uk> Perry d'Obrenan <perry.dobrenan@=
ualberta.ca> writes:
>=20
> > Does anyone know of a Macintosh application which can read Beckman
> > CEQ2000.scf files in the same way that ABI's Editview allows you to see
> > the electropherogram, run parameters, sequence text, etc.etc.
>=20
> I've looked at a Beckman file and it's claims at being SCF are stretching
> things a bit far.
>=20
> It did indeed have a valid SCF format in the strictest of senses, but in =
a
> completely useless way. dump_scf revealed the header as follows:
>=20
> [Header]
> 779314022       # magic_number
> 0               # samples
> 0               # samples_offset
> 0               # bases
> 0               # bases_left_clip
> 0               # bases_right_clip
> 0               # bases_offset
> 6               # comments_size
> 128             # comments_offset
> 2.10            # version
> 2               # sample_size
> 2               # code_set
> 171618          # private_size
> 134             # private_offset
>=20
> Ie there's no trace or base data at all - it's all stored in the private
> block.
>=20
> I don't know whether this is typical of other Beckman files, but if so th=
en I
> guess we can say that no program is likely to be able to read Beckman "sc=
f"
> files unless it has inside knowledge of the private data format.
>=20
>       James
> --
> James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 2=
13556
> 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/
>=20
> ---


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