d2a02f56a0e84d51213d44955b694ce7daace230 jnavarr5 Fri May 31 11:41:50 2019 -0700 Updating redirected links for hg18, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/human/encodeEgaspSuper.html src/hg/makeDb/trackDb/human/encodeEgaspSuper.html index fd0ab03..6cf92dc 100644 --- src/hg/makeDb/trackDb/human/encodeEgaspSuper.html +++ src/hg/makeDb/trackDb/human/encodeEgaspSuper.html @@ -1,258 +1,258 @@ <H2>Overview</H2> <P> This super-track combines related tracks from the ENCODE Gene Annotation Assessment Project (EGASP) <A HREF="http://genome.crg.es/gencode/workshop2005.html" TARGET=_BLANK> 2005 Gene Prediction Workshop</A>. The goal of the workshop was to evaluate automatic methods for gene annotation of the human genome, with a focus on protein-coding genes. Predictions were evaluated in terms of their ability to reproduce the high-quality manually assisted GENCODE gene annotations and to predict novel transcripts. <P> The <B>EGASP Full</B> track shows gene predictions covering all 44 ENCODE regions submitted before the GENCODE annotations were released. The <B>EGASP Partial</B> track shows gene predictions that cover some of the ENCODE regions, submitted before the GENCODE release. The <B>EGASP Update</B> track shows gene predictions that cover all ENCODE regions, submitted after the GENCODE release. <P> These annotations were originally produced using the hg17 assembly. </P> <P> The following gene predictions are included: <UL> <LI> -<A HREF="http://genes.mit.edu/acescan/" TARGET=_blank>ACEScan</A></LI> +<A HREF="http://hollywood.mit.edu/acescan/" TARGET=_blank>ACEScan</A></LI> <LI> <A HREF="https://www.ncbi.nlm.nih.gov/ieb/research/acembly/" TARGET=_blank>AceView</A></LI> <LI> DOGFISH-C</LI> <LI> <A HREF="http://www.ensembl.org" TARGET=_blank>Ensembl</A></LI> <LI> <A HREF="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-s1-s7" TARGET=_blank>Exogean</A></LI> <LI> <A HREF="http://compbio.fmph.uniba.sk/exonhunter/" TARGET=_blank>ExonHunter</A></LI> <LI> <A HREF="http://linux1.softberry.com/berry.phtml" TARGET=_blank>Fgenesh Pseudogenes</A></LI> <LI> <A HREF="http://linux1.softberry.com/berry.phtml" TARGET=_blank>Fgenesh++</A></LI> <LI> <A HREF="http://genome.crg.es/software/geneid/index.html" TARGET=_blank>GeneID-U12</A> </LI> <LI> <A HREF="http://opal.biology.gatech.edu/GeneMark/" TARGET=_blank>GeneMark</A></LI> <LI> <A HREF="http://www.genezilla.org/" TARGET=_blank>GeneZilla</A></LI> <LI> <A HREF="http://cbcb.umd.edu/software/jigsaw/" TARGET=_blank>JIGSAW</A></LI> <LI> <A HREF="http://mblab.wustl.edu/software/" TARGET=_blank>Pairagon/N-SCAN</A></LI> <LI> SAGA</LI> <LI> <A HREF="http://genome.crg.es/software/sgp2/index.html" TARGET=_blank>SGP2-U12</A></LI> <LI> SPIDA</LI> <LI> <A HREF="http://mblab.wustl.edu/" TARGET=_blank>Twinscan-MARS</A></LI> <LI> <A HREF="http://www.pseudogenes.org" TARGET=_blank>Yale pseudogenes</A></LI> </UL> </P> <H2>Credits</H2> <P> Click <A HREF="http://genome.crg.es/gencode/participants.html" TARGET=_blank>here</A> for a complete list of people who participated in the GENCODE project. </P> <P> The following individuals and institutions provided the data for the subtracks in this annotation: <UL> <LI> <B>AceView:</B> Danielle and Jean Thierry-Mieg, <A HREF="https://www.ncbi.nlm.nih.gov/" TARGET=_blank>NCBI</A>, National Institutes of Health. <LI> <B>DOGFISH-C:</B> David Carter, Informatics Dept., <A HREF="https://www.sanger.ac.uk/" TARGET=_blank>Wellcome Trust Sanger Institute</A>. <LI> <B>Ensembl:</B> Stephen Searle, Wellcome Trust Sanger Institute (joint <A HREF="https://www.sanger.ac.uk/" TARGET=_blank>Sanger</A>/<A HREF="https://www.ebi.ac.uk/" TARGET=_blank>EBI</A> project). <LI> <B>Exogean:</B> Sarah Djebali, Dyogen Lab, <A HREF="http://www.ens.fr/?lang=en" TARGET=_blank>Ecole Normale Supérieure</A> (Paris, France). <LI> <B>ExonHunter:</B> Tomas Vinar, <A HREF="https://cs.uwaterloo.ca/research/research-areas/bioinformatics" TARGET=_blank>Waterloo Bioinformatics</A>, School of Computer Science, University of Waterloo. <LI> <B>Fgenesh, Fgenesh++:</B> Victor Solovyev, <A HREF="https://www.royalholloway.ac.uk/computerscience/home.aspx" TARGET=_blank>Department of Computer Science</A>, Royal Holloway, London University. <LI> <B>GeneID-U12, SGP2-U12:</B> Tyler Alioto, Grup de Recerca en Informàtica Biomèdica (<A HREF="http://grib.imim.es" TARGET=_blank>GRIB</A>) at the Institut Municipal d'Investigació Mèdica (IMIM), Barcelona. <LI> <B>GeneMark:</B> Mark Borodovsky, Alex Lomsadze and Alexander Lukashin, <A HREF="https://biosciences.gatech.edu/" TARGET=_blank>Department of Biology</A>, Georgia Institute of Technology. <LI> <B>JIGSAW:</B> Jonathan Allen, Steven Salzberg group, The Institute for Genomic Research (<A HREF="https://www.jcvi.org/" TARGET=_blank>TIGR</A>) and the Center for Bioinformatics and Computational Biology (<A HREF="http://www.cbcb.umd.edu" TARGET=_blank>CBCB</A>) at the University of Maryland, College Park. <LI> <B>Pairagon/N-SCAN:</B> Randall Brown, <A HREF="http://mblab.wustl.edu/" TARGET=_blank>Laboratory for Computational Genomics</A>, Washington University in St. Louis. <LI> <B>SPIDA:</B> Damian Keefe, Birney Group, <A HREF="https://www.ebi.ac.uk/" TARGET=_blank>EMBL-EBI</A>. <LI> <B>Twinscan:</B> Paul Flicek, Brent Lab, <A HREF="http://mblab.wustl.edu/" TARGET=_blank>Washington University in St. Louis</A>. <LI> <B>ACEScan:</B> Gene Yeo, Crick-Jacobs Center for Computational Biology, <A HREF="https://www.salk.edu/" TARGET=_blank>Salk Institute</A>. <LI> <B>Augustus:</B> Mario Stanke, <A HREF="http://gobics.de/department/" TARGET=_blank>Department of Bioinformatics</A>, University of Göttingen, Germany. <LI> <B>GeneZilla:</B> William Majoros, Dept. of Bioinformatics, The Institute for Genomic Research (<A HREF="https://www.jcvi.org/" TARGET=_blank>TIGR</A>). <LI> <B>SAGA:</B> Sourav Chatterji, Lior Pachter lab, <A HREF="https://pachterlab.github.io/group.html" TARGET=_blank>Department of Mathematics</A>, U.C. Berkeley. </UL></P> <H2>References</H2> <P> Ashurst JL, Chen CK, Gilbert JG, Jekosch K, Keenan S, Meidl P, Searle SM, Stalker J, Storey R, Trevanion S <em>et al</em>. <A HREF="https://academic.oup.com/nar/article/33/suppl_1/D459/2505459" TARGET=_blank>The Vertebrate Genome Annotation (Vega) database</A>. <em>Nucleic Acids Res</em>. 2005 Jan 1;33(Database issue):D459-65. </P> <P> Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C <em>et al</em>. <A HREF="https://www.pnas.org/content/100/3/1140.full" TARGET=_blank>Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes</A>. <em>Proc Natl Acad Sci U S A</em>. 2003 Feb 4;100(3):1140-5. </P> <P> Mouse Genome Sequencing Consortium. <A HREF="https://www.nature.com/articles/nature01262" TARGET=_blank>Initial sequencing and comparative analysis of the mouse genome</A>. <em>Nature</em>. 2002 Dec 5;420(6915):520-62. </P> <P> Reymond A, Marigo V, Yaylaoglu MB, Leoni A, Ucla C, Scamuffa N, Caccioppoli C, Dermitzakis ET, Lyle R, Banfi S <em>et al</em>. <A HREF="https://www.nature.com/articles/nature01178" TARGET=_blank>Human chromosome 21 gene expression atlas in the mouse</A>. <em>Nature</em>. 2002 Dec 5;420(6915):582-6. </P> <P> Reymond A, Camargo AA, Deutsch S, Stevenson BJ, Parmigiani RB, Ucla C, Bettoni F, Rossier C, Lyle R, Guipponi M <em>et al</em>. <A HREF="https://www.sciencedirect.com/science/article/pii/S0888754302967819" TARGET=_blank>Nineteen additional unpredicted transcripts from human chromosome 21</A>. <em>Genomics</em>. 2002 Jun;79(6):824-32.</P> <P> Chatterji S, Pachter L. <A HREF="https://dl.acm.org/citation.cfm?id=974639&jmp=cit&coll=GUIDE&dl=GUIDE" TARGET=_blank>Multiple organism gene finding by collapsed Gibbs sampling</A>. <em>J Comput Biol</em>. 2005 Jul-Aug;12(6):599-608. </P> <P> Siepel A, Haussler D. <A HREF="https://dl.acm.org/citation.cfm?id=974638&coll=GUIDE&dl=GUIDE" TARGET=_blank>Computational identification of evolutionarily conserved exons</A>. <em>Proc. 8th Int'l Conf. on Research in Computational Molecular Biology</em>. 2004;177-186.</P> <H3>Augustus</H3> <P> Stanke M, Waack S. <A HREF="https://academic.oup.com/bioinformatics/article/19/suppl_2/ii215/180603" TARGET=_blank>Gene prediction with a hidden Markov model and a new intron submodel</A>. <em>Bioinformatics</em>. 2003;19(Suppl. 2):ii215-ii225.</P> <P> Stanke M, Steinkamp R, Waack S, Morgenstern B. <A HREF="https://academic.oup.com/nar/article/32/suppl_2/W309/1040489" TARGET=_blank>AUGUSTUS: a web server for gene finding in eukaryotes</A>. <em>Nucleic Acids Res</em>. 2004 Jul 1;32(Web Server issue):W309-12.</P> <H3>FGenesh++</H3> <P> Solovyev VV. "Statistical approaches in Eukaryotic gene prediction". In <em>Handbook of Statistical Genetics</em> (eds. Balding D <em>et al</em>.) (John Wiley & Sons, Inc., 2001). p. 83-127.</P> <H3>GeneID</H3> <P> Blanco E, Parra G, Guigó R. "Using geneid to identify genes". In <em>Current Protocols in Bioinformatics</em>, Unit 4.3. (eds. Baxevanis AD.) (John Wiley & Sons, Inc., 2002).</P> <P> Guigó R. <A HREF="https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.681" TARGET=_blank>Assembling genes from predicted exons in linear time with dynamic programming</A>. <em>J Comput Biol</em>. 1998 Winter;5(4):681-702. </P> <P> Guigó R, Knudsen S, Drake N, Smith T. <A HREF="https://www.sciencedirect.com/science/article/pii/002228369290130C" TARGET=_blank>Prediction of gene structure</A>. <em>J Mol Biol</em>. 1992 Jul 5;226(1):141-57.</P> <P> Parra G, Blanco E, Guigó R. <A HREF="https://genome.cshlp.org/content/10/4/511.full" TARGET=_blank>GeneID in <em>Drosophila</em></A>. <em>Genome Res</em>. 2000 Apr;10(4):511-5. </P> <H3>JIGSAW</H3> <P> Allen JE, Pertea M, Salzberg SL. <A HREF="https://genome.cshlp.org/content/14/1/142.full" TARGET=_blank>Computational gene prediction using multiple sources of evidence</A>. <em>Genome Res</em>. 2004 Jan;14(1):142-8.</P> <P> Allen JE, Salzberg SL. <A HREF="https://academic.oup.com/bioinformatics/article/21/18/3596/202486" TARGET=_blank>JIGSAW: integration of multiple sources of evidence for gene prediction</A>. <em>Bioinformatics</em>. 2005 Sep 15;21(18):3596-603.</P> <H3>SGP2</H3> <P> Guigó R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C <em>et al</em>. <A HREF="https://www.pnas.org/content/100/3/1140.full" TARGET=_blank>Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes</A>. <em>Proc Natl Acad Sci U S A</em>. 2003 Feb 4;100(3):1140-5.</P> <P> Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigó R. <A HREF="https://genome.cshlp.org/content/13/1/108.full" TARGET=_blank>Comparative gene prediction in human and mouse</A>. <em>Genome Res</em>. 2003 Jan;13(1):108-17. </P>