db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d markd Wed Apr 17 21:12:30 2024 -0700 added missing or outdated ENCODE files from the rr diff --git src/hg/htdocs/ENCODE/downloads/index.html src/hg/htdocs/ENCODE/downloads/index.html new file mode 100644 index 0000000..71ad3b3 --- /dev/null +++ src/hg/htdocs/ENCODE/downloads/index.html @@ -0,0 +1,176 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"> +<HTML> +<HEAD> + <META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1"> + <META name="description" content="UCSC Genome Browser Downloads"> + <META name="keywords" content="ENCODE, project, ENCODE project, genome, genome browser, human genome, Blat, UCSC, bioinformatics, gene prediction, SNP, EST, mRNA, NHGRI, NISC, download, downloads"> + <TITLE>UCSC Genome Browser: Downloads</TITLE> + <LINK REL="STYLESHEET" HREF="../../style/HGStyle.css"> +</HEAD> + +<BODY BGCOLOR="FFF9D2" LINK="0000CC" VLINK="#330066" ALINK="#330066"> +<A NAME="TOP"></A> + +<!-- Header Images and links --> +<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%"> + <TR> + <TH COLSPAN=2 ALIGN="left"> + <A HREF="http://www.genome.gov/10506161" TARGET=_BLANK><IMG SRC="/images/encodelogo.gif" height=50 ALT="ENCODE Project at NHGRI"></A> + + <A HREF="http://genome-test.cse.ucsc.edu/encode/"><IMG SRC="/images/encode.jpg" ALT="ENCODE Project at UCSC"></A> + </TH> + </TR> + +<!--Hotlinks bar-------------------------------------------------------> +<TABLE BORDER=0 WIDTH="100%"> + <TR> + <TH COLSPAN=2 ALIGN="left"> + </TH> + </TR> + <TR> + <TD COLSPAN=2 HEIGHT=40> + <TABLE bgcolor="000000" cellpadding="1" cellspacing="1" width="100%" height="27"> + <TR bgcolor="2636D1"> + <TD valign="middle"> + <TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 bgcolor="2636D1" height="24"> + <TR> + <TD VALIGN="middle"> + <font color="#89A1DE"> + <A class="topbar" HREF="/encode/encode.html"> + Regions </a> - + <A class="topbar" HREF="/encode/submission.html"> + Data Submission </a> - + <A class="topbar" HREF="http://genome-test.cse.ucsc.edu/encode/downloads/"> + Downloads </a> - + <A class="topbar" HREF="/cgi-bin/hgLiftOver"> + Tools </a> - + <A class="topbar" HREF="/encode/terms.html"> + Terms </a> - + <A class="topbar" HREF="/goldenPath/help/hgTracksHelp.html"> + Help </a> + </font> + </TD> + </TR> + </TABLE> + </TD> + </TR> + </TABLE> + </TD> + </TR> +</TABLE> + +<!--Downloads menu-------------------------------------------------------> +<TABLE BORDER=0 WIDTH="100%"> + <TR> + <TH COLSPAN=2 ALIGN="left"> + </TH> + </TR> + <TR> + <TD CELLPADDING=10> + <!--outer table is for border purposes--> + <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"> + <TR> + <TD> + <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"> + <TR> + <TD> + <TABLE BGCOLOR="D9E4F8" BACKGROUND="/images/hr.gif" WIDTH=100%> + <TR> + <TD> + <FONT SIZE="4"> + <b> Sequence and Annotation Downloads</b> + </FONT> + </TD> + </TR> + </TABLE> + <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0> + <TR> + <TH HEIGHT=10></TH> + </TR> + <TR> + <TD WIDTH=10> </TD> + <TD> + This page contains sequence and annotation data downloads. + <P> + For a description of the format and tables of + the annotation databases, refer to the + <A HREF="/goldenPath/gbdDescriptions.html"> + Description of the annotation database </A> + and the + <A HREF="/goldenPath/help/hgTracksHelp.html#IndivTracks"> + User's Guide</A>. + </TD> + <TD WIDTH=15></TD> + </TR> + </TABLE> + <br> + </TD> + </TR> + </TABLE> + </TD> + </TR> + </TABLE> + </TD> + </TR> +</TABLE> + +<!--Terms of Use Table-------------------------------------------------------> +<A NAME="terms"></A> +<TABLE BORDER=0 WIDTH="100%"><TR><TH COLSPAN=2 ALIGN="left"></TH></TR> + <TR><TD CELLPADDING=10> + <!--outer table is for border purposes--> + <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> + <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> + <TABLE BGCOLOR="D9E4F8" BACKGROUND="/images/hr.gif" WIDTH=100%><TR><TD> + <FONT SIZE="4"><b> Terms of Use</b></FONT> + </TD></TR></TABLE> + <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0><TR><TH HEIGHT=10></TH></TR> + <TR><TD WIDTH=10> </TD><TD> + <P> + All of the tables in the Genome Browser are freely usable for any + purpose except as indicated in the README.txt files in the download + directories. To view restrictions specific to a particular assembly, + click on the corresponding download link below and scroll to the + bottom of the page. This data was contributed by many researchers, + as listed on the Genome Browser <A + HREF="../credits.html" TARGET=_blank>credits</A> page. + Please acknowledge the contributor(s) of the data you use. + <P> + Note that specific restrictions on the use of the ENCODE + data are in place, and can be accessed <A + HREF="../terms.html">here</A>. + </TD><TD WIDTH=15></TD></TR></TABLE> + <br></TD></TR></TABLE> + </TD></TR></TABLE> +</TD></TR></TABLE> + +<!--Human Downloads-------------------------------------------------------> +<A NAME="human"></A> +<TABLE BORDER=0 WIDTH="100%"><TR><TH COLSPAN=2 ALIGN="left"></TH></TR> + <TR><TD CELLPADDING=10> + <!--outer table is for border purposes--> + <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> + <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> + <TABLE BGCOLOR="D9E4F8" BACKGROUND="/images/hr.gif" WIDTH=100%><TR><TD> + <FONT SIZE="4"><b> Downloads of the Human Genome and + Annotations </b></FONT> + </TD></TR></TABLE> + <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0><TR><TH HEIGHT=10></TH></TR> + <TR><TD WIDTH=10> </TD><TD> + <FONT SIZE="4"> + Jul. 2003 (hg16) + <UL> + <LI><A HREF="hg16/regions/"> Nucleotide Sequences</A> + <LI><A HREF="hg16/encodeProteins.fa"> Protein Sequences</A> + <LI><A HREF="hg16/liftOver/"> Coordinate conversion files</A> + <LI><A HREF="http://hgdownload.cse.ucsc.edu/goldenPath/hg16/encode/"> Annotation database</A> + <LI><A HREF="http://genome-test.cse.ucsc.edu/encode/downloads/msa/">Multiple sequence alignments</A> + </UL> + </FONT> + </TD><TD WIDTH=15></TD></TR></TABLE> + </TD></TR></TABLE> + </TD></TR></TABLE> +</TD></TR> </TABLE> + +</BODY></HTML> +