17cda45b082befcc4b38faa51661b519e5669752 lrnassar Tue Mar 17 10:53:48 2026 -0700 Feedback from CR, refs #37247 diff --git src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html index 44879d67f35..433e36b32e8 100644 --- src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html +++ src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html @@ -145,48 +145,48 @@ to search for similar nongenic sequences in ENCODE regions. The matching sequences were assessed as disabled copies of genes based on the occurrences of premature stop codons or frameshifts. The intron-exon structure of the functional gene was further used to infer whether a pseudogene was duplicated or processed (a duplicated pseudogene keeps the intron-exon structure of its parent functional gene). Small pseudogene sequences were labeled as fragments or other types.</P> <P> All pseudogenes in this track were manually curated. In the browser, the track details page shows the pseudogene type.</P> <H2>Credits</H2> <P> Augustus was written by Mario Stanke at the <A HREF="http://gobics.de/department/" TARGET=_blank>Department of -Bioinformatics</A> of the University of G�ttingen in Germany.</P> +Bioinformatics</A> of the University of Göttingen in Germany.</P> <P> Exogean was developed by Sarah Djebali and Hugues Roest Crollius from the Dyogen Lab, <A HREF="https://www.ens.psl.eu/" TARGET=_blank>Ecole -Normale Sup�rieure</A> (Paris, France) and Franck Delaplace -from the Laboratoire de M�thodes Informatiques +Normale Supérieure</A> (Paris, France) and Franck Delaplace +from the Laboratoire de Méthodes Informatiques (<A HREF="https://www.sigles.net/sigle/lami-laboratoire-des-methodes-informatiques" TARGET=_blank>LaMI</A>), (Evry, France).</P> <P> The FGenesh++ gene predictions were provided by Victor Solovyev of <A HREF="http://www.softberry.com/" TARGET=_blank>Softberry Inc.</A> <P> The GeneID-U12 and SGP2-U12 programs were developed by the -Grup de Recerca en Inform�tica Biom�dica +Grup de Recerca en Informàtica Biomédica (<A HREF="https://grib.upf.edu/" TARGET=_blank>GRIB</A>) at -the Institut Municipal d'Investigaci� M�dica (IMIM) in Barcelona. +the Institut Municipal d'Investigació Mèdica (IMIM) in Barcelona. The version of GeneID on which GeneID-U12 is based (geneid_v1.2) was written by -Enrique Blanco and Roderic Guig�. +Enrique Blanco and Roderic Guigó. The parameter files were constructed by Genis Parra and Francisco Camara. Additional contributions were made by Josep F. Abril, Moises Burset and Xavier Messeguer. Modifications to GeneID that allow for the prediction of U12-dependent splice sites and incorporation of U12 introns into gene models were made by Tyler Alioto.</P> <P> Jigsaw was developed at The Institute for Genomic Research (<A HREF="https://www.jcvi.org/" TARGET=_blank>TIGR</A>) by Jonathan Allen and Steven Salzberg, with computational gene-finder contributions from Mihaela Pertea and William Majoros. Continued maintenance and development of Jigsaw will be provided by the Salzberg group at the Center for Bioinformatics and Computational Biology (<A HREF="https://www.cbcb.umd.edu/" TARGET=_blank>CBCB</A>) at the University of Maryland, College Park.</P> @@ -212,63 +212,63 @@ <P> Stanke, M., Steinkamp, R., Waack, S. and 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>Nucl. Acids Res.</em>, <B>32</B>, W309-W312 (2004).</P> <H3>FGenesh++</H3> <P> Solovyev V.V. "Statistical approaches in Eukaryotic gene prediction". In <em>Handbook of Statistical Genetics</em> (eds. Balding D. et al.) (John Wiley & Sons, Inc., 2001). p. 83-127.</P> <H3>GeneID</H3> <P> -Blanco, E., Parra, G. and Guig�, R. +Blanco, E., Parra, G. and Guigó, R. "Using geneid to identify genes". In <em>Current Protocols in Bioinformatics</em>, Unit 4.3. (ed. Baxevanis, A.D.) (John Wiley & Sons, Inc., 2002).</P> <P> -Guig�, R. +Guigó, R. <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10072084&dopt=Abstract" TARGET=_blank>Assembling genes from predicted exons in linear time with dynamic programming</A>. J Comput Biol. <B>5</B>(4), 681-702 (1998).</P> <P> -Guig�, R., Knudsen, S., Drake, N. and Smith, T. +Guigó, R., Knudsen, S., Drake, N. and Smith, T. <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1619647&query_hl=5" TARGET=_blank>Prediction of gene structure</A>. J Mol Biol. <B>226</B>(1), 141-57 (1992).</P> <P> -Parra, G., Blanco, E. and Guig�, R. +Parra, G., Blanco, E. and Guigó, R. <A HREF="https://genome.cshlp.org/content/10/4/511.full" TARGET=_blank>GeneID in <em>Drosophila</em></A>. <em>Genome Research</em> <B>10</B>(4), 511-515 (2000).</P> <H3>Jigsaw</H3> <P> Allen, J.E., Pertea, M. and Salzberg, S.L. <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>, <B>14</B>(1), 142-8 (2004). </P> <P> Allen, J.E. and Salzberg, S.L. <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> <B>21</B>(18), 3596-3603 (2005).</P> <H3>SGP2</H3> <P> -Guig�, R., Dermitzakis, E.T., Agarwal, P., Ponting, C.P., Parra, G., +Guigó, R., Dermitzakis, E.T., Agarwal, P., Ponting, C.P., Parra, G., Reymond, A., Abril, J.F., 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> <B>100</B>(3), 1140-5 (2003).</P> <P> -Parra, G., Agarwal, P., Abril, J.F., Wiehe, T., Fickett, J.W. and Guig�, R. +Parra, G., Agarwal, P., Abril, J.F., Wiehe, T., Fickett, J.W. and 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> <B>13</B>(1), 108-17 (2003). </P>