WTD:SCF viewer with rev/compl for linux

jkb at mrc-lmb.cam.ac.uk jkb at mrc-lmb.cam.ac.uk
Fri Jan 26 04:55:45 EST 2001


In <94mpjo$5bc$1 at mercury.hgmp.mrc.ac.uk> "Forster, Robert" <ForsteR at prose.dpi.qld.gov.au> writes:

> Hello: I'm looking for a simple SCF viewer that will give me the reverse
> complement of the original read. I have a large multiple alignment file in a
> Linux program and I want to check the reads from the original data. Of
> course some of the SCF sequence data are in the opposite orientation to the
> final alignment. I would usually do this with sequencher (Mac) or Chromas
> (win) but I need a linux program. Trev doesn't seem to do rev/comp. 

Trev has this functionality, but it is currently disabled because there are
bugs when editing the trace in complemented mode. However if you do not wish
to edit then just reenable it. To do this create yourself a $HOME/.trevrc and
add the line:

add_command    {Edit.Complement}                2 18 {.trev.trace.t complement}

(Or alternatively remove the comment in $STADTABL/trevrc)

James
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/


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