If the version of readseq you use does not include the 'translate.patch'
for converting sequence characters, you will want to get that
and compile it into the readseq you use.
Then when you use readseq to convert to MSF format, you will want
to use the translation of "-" characters to the different
character "." that GCG MSF file format uses.
Find the translate patch for readseq at:
ftp://iubio.bio.indiana.edu/molbio/readseq/translate.patch
Use it this way
readseq -t-. -f=msf ...
This should correct the problem you report below.
-- Don
P.S., when I use GCG v. 8.0 distances, I get a slightly different
error message using your sample sequence:
DISTANCES for what aligned sequences ? rseq-bug.msf{*}
*** ERROR, bad sequence format in rseq-bug.msf{test1} ! ***
In article <47vm0c$ijn at ovisun.ovi.ac.za>,
Basil Allsopp <basil at ovi.ac.za> wrote:
>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
--
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu
