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assemble_shotgun... assemble4 ...BUG?

major at genome.wi.mit.edu major at genome.wi.mit.edu
Mon Feb 10 04:24:00 EST 2003

Hello group-

I've noticed some odd behavior with the 'assemble_shotgun' routine available
through the gap4 tcl api(The same assemble_shotgun routine which is used in the
assemble4 script) 

I have many gapDB's to which I would like to add fwd and rev primer sequece to.
 The primer sequence is only 20 bases in length for each primer.   These primers
each have their own file(FWDseq and REVseq, and a fofn: primers.fofn, containing
both *seq filenames) When I'm working with a gapDB via tha gap4 GUI, I can add
these short sequences in with no problem via the assembly->Normal Shotgun
Assembly menus(after changing the max_inital_match value to 14, max pads to 2
and the %mismatch to 10%).  I load primers.fofn and both REV and FWD sequences
are added to the gapDB NOT as new contigs- *NOTE* the primers ofen are
complemented or reverse complemented when being incorporated by gap4- this is fine.

The problem I'm having is that when I use assemble_shotgun via the assemble4
script, or assemble_shotgun via a modified version of this script, these same
sequences will not load into the gapDB, but are put in their own contigs...?

It appears that the assemble_shotgun interface will not change the sequence
being added(by change I mean reverse or reverse complement, etc).  When I
reverse complement the sequence in the REVseq and FWDseq files assemble_shotgun
adds them to existing contigs in the DB....as if loaded via the gap4 GUI.

My question is:  How can I get assemble_shotgun to behave like the
Assembly->Normal Shotgun Assemble feature in the GUI?  Why does assemble_shotgun
not appear to manipulate sequence in the files it is given when the GUI Normal
Shotgun Assembly does? 

Thanks in advance-

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