[Staden] Can it be made easier to use?

Mike Dyall-Smith mlds at unimelb.edu.au
Sun Apr 9 23:00:42 EST 2006

[cross-posted to sourceforge staden Package forum]

Can someone write an outline (for Mac OS X 10.4.x) of how two related .abi
files can be assembled into a contig, and edited (assume a couple of
errors over 500-800nt), in 5 minutes or less?

I try and use pregap4 and gap4 every now and then, but I find them very
frustrating. In sequencher I can drag a few .abi files together, press the
magic button, they align, and I can start editing. In pregap4/gap4 I can
spend hours, poring over the manuals, trying to find files through the X11
directory window (a cramped, and very tedious way to locate anything), and
may manage to get a couple of sequences overlapped.

The issues:
a) getting .abi files through pregap4 into gap4 seems almost impossible at
times. This shouldn't be so difficult. It either can't make a gap4
database, can't open it or puts nothing in it. Why can't pregap4 finish
then offer you the chance to open up the newly created database in gap4
(or some similar, seamless way to get to where you want to be). The file
names have to have particular prefixes/suffixes (?), the gap4 assembly
can't be used to put things into a gap4 database (?).

b)The X11 file finding window is small and cumbersome
It often doesn't remember the last place you were. Maybe a 'project'
window could be added, so the files would all be accessible from the same

I realise this software is very powerful but in its present form it is too
hard to use, even for people like me who are fairly confident with *nix. I
can't even be sure if there is a bug somewhere or if its behaviour is

Mike Dyall-Smith
Dept. Microbiology and Immunology
University of Melbourne

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