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Readseq and GCG

Mail Delivery Subsystem, by way of lonetto at cgl.ucsf.edu Michael A. Lonetto postmaster at CGL.UCSF.EDU
Mon Nov 13 17:42:34 EST 1995


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/ -----=-=-=-=-=-=-=










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