editing pet peeve

Peter Rice pmr at unst.sanger.ac.uk
Tue Mar 7 05:01:33 EST 1995

In article <Pine.3.89.9502242134.A10359-0100000 at molbio.cbs.umn.edu> jknott at MOLBIO.CBS.UMN.EDU (Julie Knott) writes:
>   While editing large contigs in gelassemble, I often add or delete one or 
>   more bases(n).  This shifts the sequence and makes every alignment to that 
>   sequence off by n bases.  I then have to move to every sequence in the 
>   contig and fix the shift.  Is there an easy way to use anchor or lock to 
>   avoid this problem?

You need to anchor all the sequences when deleting bases. The magic command is:

1 nnn ANCHOR

where "nnn" is the number of the top fragment, and 1 is the consensus.

1 nnn NOANCHOR turns it off again.

1 NOANCHOR turns off anchoring of the consensus.

When adding bases you can simply use overstrike mode (command OVER) to
overwrite a gap (there's usually one where you are inserting), or use insert
mode (command NOOVER) to insert the gap in all sequences first.

... and remember, if you make an awful mess, you can always use QUIT to
cancel the edits and start over.

Peter Rice                           | Informatics Division
E-mail: pmr at sanger.ac.uk             | The Sanger Centre
Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919                | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr    | England

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