Handling EST sequences

James Bonfield jkb at mrc-lmb.cam.ac.uk
Tue Jun 29 07:47:35 EST 1999

In article <1YA*ofI3n at news.chiark.greenend.org.uk> Tim Cutts <timc at chiark.greenend.org.uk> writes:
>One of the Staden package's huge strengths is in automation.  Almost
>all of the functionality of gap4 is available through the tcl
>interface to it, stash, although there are some missing things.  For
>instance gap4's "shuffle pads" feature is not available through the
>tcl interface, and neither is "phrap reassembly".

Phrap reassembly should be available from the scripting interface as
it's just a script itself. However it's not a C-level command added to
the interpreter. See $STADENROOT/lib/phrap/phrap.tcl to see how it

I agree with shuffle pads though. In theory it can be scripted, but
not without extensive work.

Thanks for your comments though. (It's nice to be appreciated.)


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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