Please note discussion of What does the Genome Browser do ?\n" -printf "
\n" - -printf "The information in this page allows navigation to -specific genome browsers when they are available. In the case where a -genome browser has not yet been constructed, the link for that species will -open a request form which will notify the U.C. Genome Browser staff as a request -to construct the genome browser for your species of interest. This is a new -and experimental service, we are interested to see if such requests are -many or few. Depending upon the level of activity, the expected processing -time for an assembly to appear in the genome browser should be on the order of -two weeks. +printf "
The UCSC Genome Browser provides a rapid and reliable display of any +requested portion of any genome assembly at any scale, together with dozens +of aligned annotation tracks (genes, mRNAs, CpG islands, regulation, +variation, repeats, and more). The Genome Browser stacks annotation tracks +beneath genome coordinate positions, allowing rapid visual correlation of +different types of information. The user can look at a whole chromosome to +get a feel for gene density, open a specific cytogenetic band to see a +positionally mapped disease gene candidate, or zoom in to a particular gene +to view its spliced ESTs and possible alternative splicing. The Genome Browser +itself does not draw conclusions; rather, it collates all relevant information +in one location, leaving the exploration and interpretation to the user. For +more information on using the UCSC Genome Browser please see our +help and +training +pages. +
+This page lists both whole genome assembly browsers that are available for +immediate viewing, and assemblies that are not currently available but can +be requested. +
+We are working on adding a search function to this page. Until then, please use the "find" feature of your Browser (commonly CTRL+F). +
+After searching the page, if you do not find the assembly you are +interested in, you may request it using the "Request new assembly" +button at the top of the page. Complete the request form (including the +NCBI GenBank or RefSeq assembly accession identifier). You will be notified +by email when your assembly is available for viewing in the UCSC Genome +Browser. This can take up to three weeks. The assembly browser will include +the following annotation tracks: Assembly mapping, Base position, +Gaps (when present), GC Percent, Restriction Enzymes, Tandem Duplications, +CpG Islands, RefSeq mRNAs, Repeat Masking, and, if available: +NCBI RefSeq Genes and Ensembl Genes. +
+This page is optimized for use in Firefox and Safari
\n" -printf "Please note, not all possible assemblies are shown here. There is -nothing here from the clade categories: archaea, viruses, bacteria. -This display attempts to show only whole genome assemblies. Some assemblies -have been eliminated when their total assembly size is much smaller than the -typical genome size for such species. For example, only the exome -of the organism has been sequenced. And in some cases there are too many -assemblies for the same species, for example there are over 1,000 assemblies for Homo sapiens. -
\n" - -printf "This page works best in the Firefox and Safari -web browsers. The web browsers Chrome and Edge take -almost a minute to prepare the page for use. -
\n" - -printf "Use your web browser find in page function to search -for names of interest on this page. Make the entire set visiible to allow -the search to find everything. Future enhancements to this page may include -a better search system. -
\n" - -# printf "The numbers in parenthesis following the -# Scientific name (1,234) indicate the number of assemblies available -# for that species. -#
\n" - -# my @clades = qw( primates mammals birds fish vertebrate invertebrates plants fungi ); cut -d' ' -f3,5 \ /cluster/home/hiram/kent/src/hg/makeDb/doc/asmHubs/master.run.list \ | sort | awk '{printf "%s\t%s\n", $1, $2};' > asmId.sciName sort -k1,1 -u \ /cluster/home/hiram/kent/src/hg/makeDb/doc/*AsmHub/*.orderList.tsv \ > asmId.commonName; sort -u /hive/data/outside/ncbi/genomes/reports/newAsm/*.suppressed.asmId.list \ > asmId.suppressed.list join -t$'\t' asmId.sciName asmId.commonName > asmId.sciName.commonName $srcDir/garTable.pl # add in the modal popUp request hidden window printf "