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

Index: src/hg/makeDb/trackDb/tRNAs.html
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/tRNAs.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 4 -r1.2 -r1.3
--- src/hg/makeDb/trackDb/tRNAs.html	23 Jan 2010 00:15:29 -0000	1.2
+++ src/hg/makeDb/trackDb/tRNAs.html	10 Feb 2010 23:49:46 -0000	1.3
@@ -3,13 +3,13 @@
 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
@@ -34,20 +34,20 @@
 </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>
@@ -55,14 +55,14 @@
 <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>