src/hg/makeDb/trackDb/tRNAs.html 1.3

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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retrieving revision 1.3
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--- src/hg/makeDb/trackDb/tRNAs.html	23 Jan 2010 00:15:29 -0000	1.2
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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. 
+tRNAscan-SE is an integrated program that uses tRNAscan (Fichant) and an A/B box motif detection 
+algorithm (Pavesi) 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 
+COVE</A> (Eddy) 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>
+Fichant GA, Burks C. Identifying potential tRNA genes in genomic DNA 
+sequences. <EM>J Mol Biol</EM>. 1991 Aug 5;220(3):659-71.<BR>
 </P>
 <P>
-[2]	Pavesi, A., Conterio, F., Bolchi, A., Dieci, G. and Ottonello, S. (1994) 
+Pavesi A, Conterio F, Bolchi A, Dieci G, Ottonello S. 
 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>
+<EM>Nucleic Acids Res</EM>. 1994 Apr 11;22(7):1247-56.<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>
+Eddy SR, Durbin R. RNA sequence analysis using covariance 
+models. <EM>Nucleic Acids Res</EM>. 1994 Jun 11;22(11):2079-88.<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) 
+Lowe TM, Eddy SR. 
 <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.
+<EM>Nucleic Acids Res</EM>. 1997 Mar 1;25(5):955-64.
 <P>
-Chan, P.P. & Lowe, T.M. (2009) 
+Chan PP, Lowe TM. 
 <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.
+<EM>Nucleic Acids Res</EM>. 2009 Jan;37(Database issue):D93-7.
 <P>