TFAM: the tRNA identity classifier system
TFAM TFAM is a BioPerl-based tRNA classifier that uses profile models of tRNA identity derived from the year 2000 release of the Sprinzl tRNA database (the last release with a majority of experimentally annotated tRNAs) to classify the function of unknown query tRNAs. It is useful for classifying initiator tRNAs, some lysylated isoleucine tRNAs, and the charging identity of suppressors, pseudo-tRNAs or other tRNAs with unusual structure.

NEW as of Apr., 2007 TFAM 1.3 is released. TFAM can now auto-detect anticodons in the input data and use them to detect anticodon-based conflicts with its own classifications.

Feb., 2007 TFAM 1.0 is released as both of a Web Server and standalone interface with simplified installation. Earlier installation versions of TFAM depended on The Perl Data Language (PDL). This dependency is now removed (thanks to contributions from Helena Tåquist).

Feb., 2007 TFAM 1.0 adds an improved bacterial model (version 0.2) with the ability to detect the lysylated isoleucine tRNAs in some phyla of bacteria (Thanks to work by Yuanyuan Cui and data generously provided in 2004 from Paul Higgs), and two preliminary eukaryotic and archaeal models (versions 0.1) specifically tested and released for the purpose of classifying initiator tRNAs. The use of eukaryotic and archaeal 0.1 TFAM models for any other class except initiator tRNAs has not been tested in any way!

TFAM has been cited in a recent study on classifying lysylated isoleucine tRNAs in bacteria. The authors of that study published a third-party TFAM model that can be used with TFAM 1.0. For more information see Silva et al. (2006) Differential annotation of tRNA genes with anticodon CAT in bacterial genomes. Nucleic Acids Res., 34, 6015-6022.

Anybody can create tRNA classification models that can be used with standalone interface of TFAM. See the README for more information on this and using TFAM in general.

Please send me an email with 'TFAM-list' in the subject and I will add you to a private TFAM announcement list (that only I can post to). I'll use this to notify you when new versions become available.

TFAM is known to work on UNIX type systems, but has been only tested on Linux and Mac OSX. Portability of TFAM to Windows systems is unfortunately unlikely, because it depends on the COVEMF package. COVEMF is shipped together with TFAM, you don't need to download it separately.

From this page you can obtain a GNU tarballed and gzipped or a zipped version of TFAM version 1.3.

Since TFAM 1.02 TFAM is released under the Gnu General Public License version 2.

For more information or if you should publish analyses with or modifications of TFAM, please see or cite:

D.H. Ardell and S.G.E. Andersson (2006). TFAM detects co-evolution of tRNA identity rules after lateral transfer of Histidyl-tRNA synthetase. Nucl. Acids Res. 34(3):893-904.