2e3c89f43f3bb9d386178270200d0acce9fc8050 lrnassar Fri Nov 22 17:47:13 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/firstEF.html src/hg/makeDb/trackDb/firstEF.html index c68f395..387ad5c 100644 --- src/hg/makeDb/trackDb/firstEF.html +++ src/hg/makeDb/trackDb/firstEF.html @@ -1,54 +1,54 @@ <H2>Description</H2> <P>This track shows predictions from -the <a href="http://rulai.cshl.org/tools/FirstEF/" TARGET=_blank>FirstEF</a> +the <a href="https://esefinder.ahc.umn.edu/cgi-bin/tools/ESE3/esefinder.cgi" TARGET=_blank>FirstEF</a> (<u>First</u> <u>E</u>xon <u>F</u>inder) program. <P> <P>Three types of predictions are displayed: exon, promoter and CpG window. If two consecutive predictions are separated by less than 1000 bp, FirstEF treats them as one cluster of alternative first exons that may belong to same gene. The cluster number is displayed in the parentheses of each item. For example, "exon(405-)" represents the exon prediction in cluster number 405 on the minus strand. The exon, promoter and CpG-window are interconnected by this cluster number. Alternative predictions within the same cluster are denoted by "#N" where "N" is the serial number of an alternative prediction in the cluster.</P> <P>Each predicted exon is either CpG-related or non-CpG-related, based on a score of the frequency of CpG dinucleotides. An exon is classified as CpG-related if the CpG score is greater than a threshold value, and non-CpG-related if less than the threshold. If an exon is CpG-related, its associated CpG-window is displayed. The browser displays features with higher scores in darker shades of gray/black.</P> <H2>Method</H2> <P>FirstEF is a 5' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree. The probabilistic models are optimized to find potential first donor sites and CpG-related and non-CpG-related promoter regions based on discriminant analysis. For every potential first donor site (GT) and an upstream promoter region, FirstEF decides whether or not the intermediate region can be a potential first exon, based on a set of quadratic discriminant functions. FirstEF calculates the <em>a posteriori</em> probabilities of exon, donor, and promoter for a given GT and an upstream window of length 570 bp.</P> <P>For a description of the FirstEF program and the underlying classification models, refer to Davuluri <em>et al.</em>, 2001. <H2>Credits</H2> <P>The predictions for this track are produced by <a href="https://medicine.osu.edu/bmi/Pages/index.aspx" TARGET=_blank>Ramana V. -Davuluri</a> of Ohio State University and <a href="http://rulai.cshl.org/" TARGET=_blank>Ivo Grosse and +Davuluri</a> of Ohio State University and <a href="https://esefinder.ahc.umn.edu/cgi-bin/tools/ESE3/esefinder.cgi" TARGET=_blank>Ivo Grosse and Michael Q. Zhang</a> of Cold Spring Harbor Lab. <H2>References</H2> <P> Davuluri RV, Grosse I, Zhang MQ. <A HREF="https://www.nature.com/articles/ng780" TARGET=_blank>Computational identification of promoters and first exons in the human genome</A>. <em>Nat Genet</em>. 2001 Dec;<B>29</B>(4):412-7.</P>