[BiO BB] GCG problem

Iddo Friedberg idoerg at cc.huji.ac.il
Tue Oct 16 07:05:33 EDT 2001

On Tue, 16 Oct 2001, nikhil gadewal wrote:

: Hi all,
:      How to can connect the online sequence data
: from swissprot to the GCG package

1) Save the data as text, NOT from the NiceProt page, but rather from
the text page. (When you get an online entry from SwissProt, you usually
get a fancy web page. Hit the link at the bottom to get the text entry).

2) In the text file you have just created, substitute all consecutive dots
(..) with dashes or underscores. This is because GCG treats consecutive
dots as a documentation/sequence seperator. On a UNIX system just do:
sed 's/\.\./-/g' swissentry.txt > gcgentry.sw

3) Now, using your favorite editor, just before the sequence, add a ".."
in a seperate line. This functions as the seperator between documentation
and the sequence.

4) Use GCG's REFORMAT on your file, to add all those weird unprintables
GCG likes in its files.

5) In the first couple of times you are doing this, check the resulting
file with your favorite editor. Just to make sure no documentation entered
the sequence area, or vice-versa.

Hope this helps. Feel free to email me if problems occur.



Iddo Friedberg                                  | Tel: +972-2-6757374
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |

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