Re: [Artemis-users] ACT comparisons

[Tim Carver]

Hi Magdalen

Sorry to hear you are having trouble with WebACT. I have tried it a couple
of times and it is working for me. It may be a temporary glitch or possibly
an issue with the size of the sequence. It may be worth trying again?

Regards
Tim


On 2/16/11 3:34 PM, Bossers, Alex alex.boss...@wur.nl wrote:

 Magdalen,
 not sure if its supported but we successfully use MUMmer locally (or blast+)
 to generate the required comparison files.
 Best wishes,
 Alex
 
 
 Van: artemis-users-boun...@sanger.ac.uk [artemis-users-boun...@sanger.ac.uk]
 namens Magdalen Lindeberg [m...@cornell.edu]
 Verzonden: woensdag 16 februari 2011 15:32
 Aan: artemis-users@sanger.ac.uk
 Onderwerp: [Artemis-users] ACT comparisons
 
 After years of using the ³Generate² feature at WebACT
 http://www.webact.org/WebACT/generate for generating ACT readable comparison
 files, my recent attempts to generate comparisons with this feature have not
 been successful (basically, the comparison generator never concludes the job).
 Fortunately, I can get results with DoubleACT, but the output is not as
 convenient.
 
 Does anyone know if WebACT is still being supported?  No one is responding to
 the ³contact us² link.
 
 thanks,
 Magdalen
 
 Magdalen Lindeberg PhD
 Department of Plant Pathology and Plant-Microbe Interactions
 302A Plant Science Building
 Cornell University
 Ithaca NY 14853
 
 http://pseudomonas-syringae.org
 http://www.citrusgreening.org
 
 
 
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[artemis-users] ACT comparisons -

[Duffield Melanie L]

Hello,

I am trying to do an ACT comparison using big_blast on two constructions of
the same partial genome (one with 4 contigs and one with 3 to see where the
various pieces have been joined together).  I was therefore expecting large
blocks of identical sequence showing rearrangement etc.  However, I seem to
be getting loads of small blocks.  I think that of this is due to multiple
repeat elements but I was wondering if it was something to do with the
window size used by blastn or the block size by big_blast.  Does anyone have
any suggestions on how to improve the layout?

Thanks in advance
Melanie Duffield
Bioinformatics
Biomedical Sciences
Porton Down
Wilts
SP4 0JQ

Tel (1)980 614364
Fax (1)980 614307


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