198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html index ab0e231d4bb..44879d67f35 100644 --- src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html +++ src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html @@ -84,31 +84,31 @@ reduced, leading to increasingly complex objects. This process enables the production of alternative transcripts from initial HSPs.</P> <H3>FGenesh++</H3> <P> FGenesh++ predictions are based on hidden Markov models and protein similarity to the NR database. For more information, see the reference below. <H3>GeneID-U12</H3> <P> The GeneID program predicts genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using position weight arrays (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the scores -of the defining sites plus the the log-likelihood ratio of a Markov model for +of the defining sites plus the log-likelihood ratio of a Markov model for coding DNA. Finally, the gene structure is assembled from the set of predicted exons, maximizing the sum of the scores of the assembled exons. The modified version of GeneID used to generate the predictions in this track incorporates models for U12-dependent splice signals in addition to U2 splice signals.</P> <P> The GeneID subtrack shows all GeneID genes. Only U12 introns and their flanking exons are displayed in the GeneID U12 subtrack. Exons flanking predicted U12-dependent introns are assigned a type attribute reflecting their splice sites, displayed on the details page of the GeneID U12 subtrack as the "Alternate Name" of the item composed of the intron plus flanking exons.</P> <H3>Jigsaw</H3> @@ -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 Göttingen in Germany.</P> +Bioinformatics</A> of the University of G�ttingen 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 Supérieure</A> (Paris, France) and Franck Delaplace -from the Laboratoire de Méthodes Informatiques +Normale Sup�rieure</A> (Paris, France) and Franck Delaplace +from the Laboratoire de M�thodes 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 Informàtica Biomèdica +Grup de Recerca en Inform�tica Biom�dica (<A HREF="https://grib.upf.edu/" TARGET=_blank>GRIB</A>) at -the Institut Municipal d'Investigació Mèdica (IMIM) in Barcelona. +the Institut Municipal d'Investigaci� M�dica (IMIM) in Barcelona. The version of GeneID on which GeneID-U12 is based (geneid_v1.2) was written by -Enrique Blanco and Roderic Guigó. +Enrique Blanco and Roderic Guig�. 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 Guigó, R. +Blanco, E., Parra, G. and Guig�, 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> -Guigó, R. +Guig�, 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> -Guigó, R., Knudsen, S., Drake, N. and Smith, T. +Guig�, 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 Guigó, R. +Parra, G., Blanco, E. and Guig�, 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> -Guigó, R., Dermitzakis, E.T., Agarwal, P., Ponting, C.P., Parra, G., +Guig�, 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 Guigó, R. +Parra, G., Agarwal, P., Abril, J.F., Wiehe, T., Fickett, J.W. and Guig�, 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>