[Bioperl-l] frac_aligned_query returning results >1.
thiago.venancio at gmail.com
Fri Mar 2 11:14:20 EST 2007
Great to know you fixed the problem.
I have updated the SearchUtils and seems to be correct now.
On 3/2/07, Sendu Bala <bix at sendu.me.uk> wrote:
> Thiago Venancio wrote:
> > Hi Sendu and Chris,
> > Thanks for the help.
> > As I mentioned, I have updated my SearchUtils file from:
> > <
> > I am also using the lates BioPerl version, installed from CPAN.
> > Please find a buggy blast report attached.
> > In this case, the frac_aligned_query() outputs "1.04", but I have others
> > with " 1.57" for example.
> > Just for a quantitative aspect, I got ">1" values in only 61 / 53,377.
> Many thanks for that.
> I've committed another fix for SearchUtils so please get revision 1.23
> and try again. Hopefully all 61 will no longer be >1, but if any are
> please send me sample blast files again.
> For anyone interested, the bug was due to a completely unbelievable
> oversight on my part in the contig merging algorithm: I forgot to deal
> with contigs that were fully contained by others. Wow!
"The way to get started is to quit talking and begin doing."
Thiago Motta Venancio, MSc
PhD student in Bioinformatics
University of Sao Paulo
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