a tool for tiling-array data analysis

SAKURAI, Tetsuya stetsuya at gsc.riken.jp
Thu Feb 24 02:19:07 EST 2005


Dear all,

I have released an automatic-annotation program for whole-genome
tiling-array data. The program named ARTADE and its source program is
now available at the following web-site.

http://omicspace.riken.jp/ARTADE/

ARTADE calculates gene structures (exon/intron structure), their
expression levels, and statistical significances of their expressions,
based both on the genomic sequence data and array data. ARTADE
automatically predicts unknown gene structures in the inter-genic
regions where no known gene exists. In the prediction process, ARTADE
calculates the likelihood of the structure based on a Markov model, and
thus, predicts gene splice points accurately, and overcome the
disadvantages of conventional threshold-based prediction methods.

You can use it on various platforms including Windows, Mac, Linux, 64bit
machines, because the program is written in pure C++, and does not
require any additional library such as STL. I designed its minimum
memory requirement is 512MB, where it is possible to perform a whole
chromosomal analysis in a single run. However I recommend 1GB memory for
maximizing its performance.

So far, ARTADE is applicable to Arabidopsis thaliana data only. I am
planning to release ARTADE for mouse and other species until the end of
this year.

You can browse examples of predicted genes by ARTADE on our GPS database
system at the web-site.

Best,

Tetsuro Toyoda, ph.D.
Genomic Sciences Center, RIKEN, Japan.
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