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fragment assemblyREAD/NEW

Jasper Rees - Oxford University jrees at vax.oxford.ac.uk
Tue Mar 28 06:40:07 EST 1995


In article <Pine.SOL.3.91.950327160104.15968A-100000 at terre.IRCM.UMontreal.CA>, duhaimj at IRCM.UMontreal.CA (SI-Johanne Duhaime) writes:
> 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?

To reverse the whole contig, you need to anchor all the sequences, then reverse
the contig, then (optionally) sort the contig, then unanchor it all.

Thus, control Z to get to command mode, then:
 
:1 6 ANCHOR
:REVERSE
:SORT
:1 6 UNANCHOR

There doesn't seem a way to anchor all the gels *without* knowing the number
of gels in the contig.

A single command (FLIP) that did all of these in one command was in one of my
suggested lists of enhancements for Gelassemble recently to GCG, but this does
what you want now.

Note: (Irv?) it seems to me that Gelmerge flips the contig often when it should
have flips the new sequence, without looking at why this is exactly I would say
its a problem with deciding which to reverse and complement (though I can see
other logical reasons to why this should be happening to). 

> Thank you
> Johanne Duhaime
> IRCM
> duhaimj at ircm.umontreal.ca

regards,   jasper

D Jasper G Rees  MA DPhil                  The Bionic Paradox:
Wellcome Senior Research Fellow            "For every positive reference to the
The Sir William Dunn School of Pathology   Human Genome Mapping Project there is
Oxford University                          an equal and opposite reference to
South Parks Road                           Arnold Schwarzengger"
Oxford, OX1 3RE, United Kingdom

Tel:  +44 1865 275567
FAX:  +44 1865 275501               Email:  Jasper.Rees at Pathology.Oxford.Ac.UK




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