Olson's sequence editor: file format for protein multisequence

Dan Davison Davison at UH.EDU
Sat Sep 5 12:52:39 EST 1992


Don Gilbert said:
> It has always been a trial to get sequence data from other sources
> into the Olsen editor, which was designed mainly for entering
> data from keyboard.   At one point, it would only accept raw sequence
> (as you found readseq making) in single files/sequence using a special
> command (I don't recall what).  The version you have may also read in
> multi-sequence files that are in Genbank format, but I don't recall
> what the commands for that might be.  The default input format it is
> looking for is it's own special binary format, which readseq is not
> able to reproduce.

A couple things.  READSEQ should not say "Olsen" then, but say "Olsen
text" or something. This confuses a lot of people who think it
produces the binary file.

The command to read a plain text file into the editor is
        LOAD/NUC FILE.EXT
The command to read a GenBank file into the editor is
        LOAD/GENBANK FILE.EXT
but you will have to hit "return" THREE times for EACH sequence read
in.

In both cases you must be in a olsen file for the LOAD command to
work. If necessary, create a dummy first sequence in the editor.


I have a program which I am willing to share on request called
TRANSFER, written by Jack Chappelear and myself. It reads and writes
Olsen files, and can take data from binary Olsen files and write Paup
NEXUS format, Phylip 3.3 format, a pseudo-GenBank format, and about a
dozen others.  It is a VMS *only* executable and will run only on VMS
version 5 or greater.  

dan
-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison at uh.edu/DAVISON at UHOU

-----RIP Isaac Asimov 1920-1992     I'll miss him --------------------

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.





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