IUBio

Readseq and GCG

Basil Allsopp basil at ovi.ac.za
Fri Nov 10 09:01:48 EST 1995


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



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