ProMED: a global early warning system for disease.

We have earlier published an automated statistical classifier of tRNA function called TFAM. Unlike tRNA gene-finders, TFAM uses information from the total sequences of tRNAs and not just their anticodons to predict their function. Therefore TFAM has an advantage in predicting initiator tRNAs, the amino acid charging identity of nonstandard tRNAs such as suppressors, and the former identity of pseudo-tRNAs. In addition, TFAM predictions are robust to sequencing errors and useful for the statistical analysis of tRNA sequence, function and evolution. Earlier versions of TFAM required a complicated installation and running procedure, and only bacterial tRNA identity models were provided. Here we describe a new version of TFAM with both a Web Server interface and simplified standalone installation. New TFAM models are available including a proteobacterial model for the bacterial lysylated isoleucine tRNAs, making it now possible for TFAM to correctly classify all tRNA genes for some bacterial taxa. First-draft eukaryotic and archaeal models are also provided making initiator tRNA prediction easily accessible genes to any researcher or genome sequencing effort. The TFAM Web Server is available at http://tfam.lcb.uu.se

[1]  Francisco J. Silva,et al.  Differential annotation of tRNA genes with anticodon CAT in bacterial genomes , 2006, Nucleic acids research.

[2]  S. Andersson,et al.  TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase , 2006, Nucleic acids research.

[3]  Tsutomu Suzuki,et al.  molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. , 2005, Molecular cell.

[4]  J. Chakrabarti,et al.  Identity elements of archaeal tRNA. , 2005, DNA research : an international journal for rapid publication of reports on genes and genomes.

[5]  O. Nureki,et al.  Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Sergey Steinberg,et al.  Compilation of tRNA sequences and sequences of tRNA genes , 2004, Nucleic Acids Res..

[7]  P. Higgs,et al.  Comparison of tRNA and rRNA Phylogenies in Proteobacteria: Implications for the Frequency of Horizontal Gene Transfer , 2004, q-bio/0404030.

[8]  Y. Mechulam,et al.  Functional Molecular Mapping of Archaeal Translation Initiation Factor 2* , 2004, Journal of Biological Chemistry.

[9]  G. Björk,et al.  Enzymatic conversion of cytidine to lysidine in anticodon of bacterial tRNAIle – an alternative way of RNA editing , 2004 .

[10]  Dean Laslett,et al.  ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. , 2004, Nucleic acids research.

[11]  Henri Grosjean,et al.  tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. , 2002, RNA.

[12]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[13]  R. Durbin,et al.  RNA sequence analysis using covariance models. , 1994, Nucleic acids research.

[14]  Yoshiyuki Kuchino,et al.  Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification , 1988, Nature.

[15]  G. Björk,et al.  Enzymatic conversion of cytidine to lysidine in anticodon of bacterial isoleucyl-tRNA--an alternative way of RNA editing. , 2004, Trends in biochemical sciences.

[16]  K. Watanabe,et al.  Structural feature of the initiator tRNA gene from Pyrodictium occultum and the thermal stability of its gene product, tRNA(imet). , 1996, Biochimie.