fragment assembly

SI-Johanne Duhaime duhaimj at IRCM.UMontreal.CA
Mon Mar 27 16:31:33 EST 1995

Good afternoon

I have the following question.

A user wants to assemble fragments of a sequence. He also have the "seed" 
sequence which is a known sequence.

Giving the seed sequence and the fragments for assembly, he used the 
assembly package.  He includes his seed sequence because the fragment 
does not necessairly overlap.
But the result contains  the seed sequence inverted.
The user wants this sequence to be the master for the assembly and be on 
the given sens.

Exemple of the work

Contig: xxxx

   6       f1                               +-->
   5       f2                        +--->
   4       f3                    <---+
   3       f4               +-->
   2       seed        <------------------------------------+
   C       CONSENSUS   <------------------------------------+
                       0         600       1200       1800       2400

seed has be inverted.

What can we do to keep that one intact?
Thank you
Johanne Duhaime
duhaimj at ircm.umontreal.ca

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