seqapp multiple seq. editing

Don Gilbert gilbertd at bio.indiana.edu
Tue Sep 9 13:37:32 EST 1997


Robin,

It isn't possible to do that with SeqApp, but one can do it
with the successor program, SeqPup.  In the SeqPup program,
you do this using masks, as per  
  -- set your alignment view to one of 4 mask levels 
   (Select mask 1, mask 2, ... in the View popup).
  -- use mouse to highlight the area you want to cut.  You can
  drag the mouse over the top index bar to select all bases
  in a column of multiple sequences.
  -- choose the Sequence/Seq Masks/Invert mask menu command.  This
  will turn the mask into those bases you want to keep.
  -- choose the Sequence/Seq Masks/Compress by mask menu command.
  This removes your unwanted bases.

Find SeqPup at ftp://iubio.bio.indiana.edu/molbio/seqpup/ and also
at mirrors such as 
  ftp://ftp.funet.fi/pub/sci/molbio/iubiomolbio 
  ftp://ftp.sunet.se/pub/molbio
  ftp://ftp.uam.es/pub/mirror/molbio
  ftp://ftp.ddbj.nig.ac.jp/pub/mirror/IUBIO/molbio
  ftp://ftp.gdbnet.ad.jp/ftpsync/ftp.bio.indiana.edu/ 

-- Don

In article <rsperry-0909971417060001 at bhmmac2.mr.ic.ac.uk>,
Robin Perry <rsperry at ic.ac.uk> wrote:
>Is it possible to delete the first 40 bases from multiple sequence
>aligments to 'trim' the overlaps in a single step rather than having to do
>it individually to each sequence?  I can select the region I want to
>delete but can't delete it (the clear command is dimmed) with or without
>the edit lock on.
>
>Robin (rsperry at ic.ac.uk)
>
>-- 
>Mr R.S. Perry         
>Earth Resources Engineering
>Imperial College
>London
>UK
>
>email: rsperry at ic.ac.uk


--
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu



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