src/hg/makeDb/trackDb/tRNAs.html 1.2

Index: src/hg/makeDb/trackDb/tRNAs.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/tRNAs.html,v
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 <H2>Description</H2>
 <P>
 This track displays tRNA genes predicted by using 
 <A HREF="http://lowelab.ucsc.edu/tRNAscan-SE/" TARGET=_blank>tRNAscan-SE</A> v.1.23. 
 </P>
 <P>
 tRNAscan-SE is an integrated program that uses tRNAscan [1] and an A/B box motif detection 
 algorithm [2] as pre-filters to obtain an initial list of tRNA candidates. 
 The program then filters these candidates with a covariance model-based 
 search program <A HREF="ftp://selab.janelia.org/pub/software/cove/" TARGET=_blank>
 COVE</A> [3] to obtain a highly specific set of primary sequence 
 and secondary structure predictions that represent 99-100% of true tRNAs 
 with a false positive rate of fewer than 1 per 15 gigabases.</P>
 <P>
 Detailed tRNA annotations for eukaryotes, bacteria, and archaea are available at
 <A HREF="http://gtrnadb.ucsc.edu" TARGET=_blank>Genomic tRNA Database (GtRNAdb)</A>. 
 </P>
 <P>
+What does the tRNAscan-SE score mean?  Anything with a score above 20 bits is likely to be
+<I>derived</I> from a tRNA, although this does not indicate whether the tRNA gene still encodes a 
+functional tRNA molecule (i.e. tRNA-derived SINES probably do not function in the ribosome in translation).
+For vertebrate tRNAs, we believe a score of >60.0 (bits) are likely to encode functional tRNA genes, and 
+those with scores below ~45 have sequence or structural features that indicate they probably are
+no longer involved in translation.  tRNAs with scores between 45-60 bits are in the "grey" zone, and may
+or may not have all the required features to be functional.  In these cases, tRNAs should be inspected
+carefully for loss of specific primary or secondary structure features (usually in alignments with other
+genes of the same isotype), in order to make a better educated guess.  These rough score range guides 
+are not exact, nor are they based on specific biochemical studies of atypical tRNA features,
+so please treat them accordingly.
+</P>
+<P>
 Both tRNAscan-SE and GtRNAdb are maintained by the 
 <A HREF="http://lowelab.ucsc.edu" TARGET=_blank>Lowe Lab</A> at UCSC.
 </P>
 
 <H2>Credits</H2>
 <P>
 [1]	Fichant, G.A. and Burks, C. (1991) Identifying potential tRNA genes in genomic DNA 
 sequences. <EM>J Mol Biol</EM> <B>220</B>:659-671.<BR>
 </P>
 <P>
 [2]	Pavesi, A., Conterio, F., Bolchi, A., Dieci, G. and Ottonello, S. (1994) 
 Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep 
 weight matrix analysis of transcriptional control regions. 
 <EM>Nucleic Acids Res.</EM> <B>22</B>:1247-1256.<BR>
 </P>
 <P>
 [3]	Eddy, S.R. and Durbin, R. (1994) RNA sequence analysis using covariance 
 models. <EM>Nucleic Acids Res.</EM> <B>22</B>:2079-2088.<BR>
 </P>
 <P>
 Cove-predicted tRNA secondary structures were rendered by NAVIEW (c) 1988 Robert E. Bruccoleri 
 </P>
 
 <H2>References</H2>
 <P>
 When making use of these data, please cite the following articles:</P>
 <P>
 Lowe, T.M. & Eddy, S.R. (1997) 
 <A HREF="http://www.ncbi.nlm.nih.gov/pubmed/9023104?dopt=Abstract" TARGET=_blank>tRNAscan-SE: A program for
 improved detection of transfer RNA genes in genomic sequence.</A>
 <EM>Nucl. Acids Res.</EM> <B>25</B>: 955-964.
 <P>
 Chan, P.P. & Lowe, T.M. (2009) 
 <A HREF="http://nar.oxfordjournals.org/cgi/content/abstract/gkn787" TARGET=_blank>GtRNAdb: A database 
 of transfer RNA genes detected in genomic sequence.</A>
 <EM>Nucl. Acids Res.</EM> <B>37</B>(Database issue):D93-D97.
 <P>