This is an annoucement for the initial release of of tRNAscan-SE
(version 1.0), a new program for the detection of transfer RNAs in
genomic DNA sequence. It was implemented to meet the needs of the
genome analysis community (speed & high selectivity), but is also
appropriate for general use.
The program combines the specificity of the SCFG-based covariance
model probabilistic RNA prediction method (Eddy & Durbin, 1994) with
the speed and sensitivity of tRNAscan 1.3 (Fichant & Burks, 1991) and
an implementation of an algorithm described by Pavesi and colleagues
(1994). Please refer to the links below for more information on the
program algorithms and references.
By our tests, tRNAscan-SE detects ~99% of eukaryotic nuclear or
prokaryotic tRNA genes with a false positive rate of less than one per
15 gigabases (excluding tRNA-derived pseudogenes), and a search speed
of about 30 kbp/second.
The complete source code is available on our lab homepage at
http://genome.wustl.edu/eddy/
or directly by anonymous ftp at
ftp://genome.wustl.edu/pub/eddy/tRNAscan-SE.tar.Z
The source should run on any UNIX system with a C compiler
and Perl 5.0 (or later) installed.
We also have a compute server on the web for on-line
tRNA analysis:
http://genome.wustl.edu/eddy/tRNAscan-SE/
(query sequences for on-line analysis are limited to 1 million bp due
to browser constraints)
Links to an on-line (HTML) version of the user manual and man pages
are also available on the lab homepage and the analysis compute server
page.
Comments, bug reports, etc. are welcome.
A paper describing the program and its analysis of six complete or
partial genomes has been submitted. Preprints are available on
request (available in hard copy or MS Word format).
Thank you,
Todd Lowe
Sean Eddy
Dept. of Genetics,
Washington University School of Medicine
{lowe,eddy}@genetics.wustl.edu
