The question has been correctly answered below as I know to my cost, having
been around this problem at least twice on separate occasions and now being
permanently bald on top!
B
In article <199511132241.OAA10959 at socrates.ucsf.EDU>,
postmaster at CGL.UCSF.EDU (Mail Delivery Subsystem, by way of
lonetto at cgl.ucsf.edu (Michael A. Lonetto)) wrote:
> Sorry for posting this, mail to the sender bounced:
>> Sequences not recognized because they are not quite right.
>> Two problems: 1) GCG uses "." for gaps, this file has "-". This can
> be fixed with a text editor search/replace.
>> 2) Checksum problem. This can be fixed by running it through
> "reformat -msf gde842_9.msf{*}"
>> Note that if you run reformat (at least through V8.0) without first
> changing the gap character it will remove all your gaps (probably
> not what you want).
>> The third problem is that ReadSeq saves all MSF file as nucleotide, so
> protein files have to have type changed manually (not a problem here).
>>> >Does anyone know why MSF files formatted by readseq are not recognized by GCG
> >Version 8.1? (I don't know whether they were recognized by earlier versions).
> >
> >The file test.msf as written by readseq (through gde) is as follows:
> >
> > gde842_9 MSF: 100 Type: N January 01, 1776 12:00 Check: 9397 ..
> >
> > Name: test1 Len: 100 Check: 1581 Weight: 1.00
> > Name: test2 Len: 100 Check: 6389 Weight: 1.00
> > Name: test3 Len: 100 Check: 1427 Weight: 1.00
> >
> >//
> >
> > test1 AAACGATGCA CATATGTATT GTGCTCTAGA TACAGCATCA ---AGCTCTA
> > test2 AAATGATGCA CACATGTACT GTGCTTTAGA TACAGCACAA CAGAGTGCTA
> > test3 AAAAAGTGGT GCGGAATCTC TGGCAGCTAT TACCCGCGAC GCTAACATTA
> >
> > test1 CTGCAGGAGC AACT------ ACATCTGTTA TGGTAAAAAA TGAAAATTTA
> > test2 CTAATGGTGC AACATTAGCT TCATCTGTTA TGATAAAAAA TGAAAATTTA
> > test3 CTGAG----- -------ACC AATTACTTCG TAGTCAAAAT TGAGAAATTA
> >
> >
> >If I try to use "distances" on this file I get:
> >
> > *** ERROR, bad sequence format in test.msf ! ***
> > *** No files in test.msf ! ***
> >
> >Thanks in advance to anyone who can help.
> >
> >--
> >---
> >Basil Allsopp | E-mail basil at ovisun.ovi.ac.za> >Onderstepoort Veterinary Institute | Phone +27 12 5299385
> >Onderstepoort 0110, South Africa | Fax +27 12 5299431
>> -------------=-=-=-=-=-=-=-------------=-=-=-=-=-=-=-------------
> Michael Lonetto ** 415-476-1493 ** lonetto at cgl.ucsf.edu> UCSF Depts. of Stomatology and Micro.,San Francisco,CA 94143-0512
> =-=-=-=-=-=-=----- http://terminator.ucsf.edu/ -----=-=-=-=-=-=-=
--
Bernie Cohen Phone (+44) (0)141 339 8855 ext. 5103/5101
Molecular Genetics Fax 330 5994
University of Glasgow
56 Dumbarton Rd,
Glasgow G11 6NU
Scotland, UK.
