src/hg/makeDb/trackDb/nscanGene.html 1.5

Index: src/hg/makeDb/trackDb/nscanGene.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/nscanGene.html,v
retrieving revision 1.4
retrieving revision 1.5
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--- src/hg/makeDb/trackDb/nscanGene.html	2 Jul 2009 21:21:46 -0000	1.4
+++ src/hg/makeDb/trackDb/nscanGene.html	19 Apr 2010 04:34:01 -0000	1.5
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 <H2>Description</H2>
 <P>
 This track shows gene predictions using the N-SCAN gene structure prediction
 software provided by the Computational Genomics Lab at Washington University 
 in St. Louis, MO, USA.
 </P>
 
 <H2>Methods</H2>
 <P>
 N-SCAN combines biological-signal modeling in the target genome sequence along
 with information from a multiple-genome alignment to generate de novo gene
 predictions. It extends the TWINSCAN target-informant genome pair to allow for
 an arbitrary number of informant sequences as well as richer models of
 sequence evolution. N-SCAN models the phylogenetic relationships between the
 aligned genome sequences, context-dependent substitution rates, insertions,
 and deletions.
 </P>
 <P>${informant}</P>
 
 <H2>Credits</H2>
 <P>
 Thanks to <A HREF="http://mblab.wustl.edu/" 
 TARGET=_blank>Michael Brent's Computational Genomics Group</A> at Washington 
 University St. Louis for providing this data.
 </P>
 <p>
 Special thanks for this implementation of N-SCAN to Aaron Tenney in
 the Brent lab, and Robert Zimmermann, currently at Max F. Perutz
 Laboratories in Vienna, Austria.
 </p>
 
 <H2>References</H2>
 <P>
 Gross SS, Brent MR.
 <A HREF="http://www.liebertonline.com/doi/abs/10.1089/cmb.2006.13.379" TARGET=_blank>Using
 multiple alignments to improve gene prediction</A>. In
 <em>Proc. 9th Int'l Conf. on Research in Computational Molecular Biology</em>
 (RECOMB '05):374-388 and <em>J Comput Biol</em>. 2006 Mar;13(2):379-93.
 </P>
 <P>
 Korf I, Flicek P, Duan D, Brent MR.
 <A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/suppl_1/S140" TARGET=_blank>Integrating genomic homology into gene structure prediction</A>.
 <em>Bioinformatics</em>. 2001 Jun 1;17(90001):S140-8.</P>
 <P>
 van Baren MJ, Brent MR.
 <A HREF="http://www.genome.org/cgi/content/abstract/16/5/678"
 TARGET=_blank>Iterative gene prediction and pseudogene removal improves
 genome annotation</A>.
 <EM>Genome Res</EM>. 2006 May;16(5):678-85.</P>
+<P>
+Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM,
+Rusch DB, Town CD <EM>et al</EM>.
+<A HREF="http://nar.oxfordjournals.org/cgi/content/abstract/31/19/5654" TARGET=_blank>
+Improving the <EM>Arabidopsis</EM> genome annotation using maximal transcript 
+alignment assemblies.</A>
+<EM>Nucleic Acids Res</EM> 2003 Oct 1;31(19):5654-66.</P>