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HYPHY Package >> HyPhy feedback >> HIV recombinants http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1278489898 Message started by Pat on Jul 7th, 2010 at 1:04am |
Title: HIV recombinants Post by Pat on Jul 7th, 2010 at 1:04am
I have been using SCUEAL to subtype some complex HIV recombinants. For a number of sequences, each time I run the same sequence through the programme, it comes back with a different result. What is the reason for this and is there any way it can be resolved? Thanks
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Title: Re: HIV recombinants Post by Sergei on Jul 7th, 2010 at 5:41am
Hi Pat,
SCUEAL is a randomized algorithm, so some variation in output is expected. I presume that the differences that you see are not that a particular strain is reported as recombinant in one run and a pure subtype in another, but rather that the location and (possibly) the number of breakpoints may differ slightly between two runs. The latter is normal -- the online version of SCUEAL has been tuned to achieve a tradeoff between speed and accuracy on complex recombinants (these take a long time to run in order to map all the breakpoints). Can you provide an example of two different outputs (preferably links to result pages), so that I may be able to give you more specific advice? Sergei |
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