3a5369a02eabb119a6265910fda1ad76be3cba5f kuhn Fri Jan 24 11:48:14 2020 -0800 adding hyphen diff --git src/hg/htdocs/FAQ/FAQtracks.html src/hg/htdocs/FAQ/FAQtracks.html index 1df5044..267fb62 100755 --- src/hg/htdocs/FAQ/FAQtracks.html +++ src/hg/htdocs/FAQ/FAQtracks.html @@ -1,30 +1,30 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser FAQ" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Frequently Asked Questions: Genome Browser Tracks</h1> <h2>Topics</h2> <ul> <li><a href="#tracks0">List of tracks available for a specific assembly</a></li> <li><a href="#tracks1">Database/browser start coordinates differ by 1 base</a></li> -<li><a href="#tracks2">mRNA associated results</a></li> +<li><a href="#tracks2">mRNA-associated results</a></li> <li><a href="#tracks3">Correspondence of Genome Browser mRNA positions to those of OMIM genes</a></li> <li><a href="#tracks4">Position changes of features</a></li> <li><a href="#tracks6">Evaluating possible alternative splices</a></li> <li><a href="#tracks7">Matching exons and protein sequence</a></li> <li><a href="#tracks9">Cause of duplicated gene</a></li> <li><a href="#tracks11">Protein doesn't begin with methionine</a></li> <li><a href="#tracks12">Doing an orthology track analysis of a protein</a></li> <li><a href="#tracks14">Quality benchmarks for predicted genes</a></li> <li><a href="#tracks15">Display conventions for gene prediction tracks</a></li> <li><a href="#tracks16">Viewing detailed displays in conservation tracks</a></li> <li><a href="#tracks17">Negative strand coordinates in PSL files</a></li> <li><a href="#tracks18">Inconsistency in stop codon treatment in GTF tracks</a></li> <li><a href="#tracks19">Obtaining clones referenced in Genome Browser</a></li> <li><a href="#tracks20">Locating centromeres and telomeres</a></li> @@ -61,31 +61,31 @@ prefer to see the one-based start coordinates, you will always need to add 1 to each start coordinate.</p> <p> If you submit data to the browser in position format (chr#:##-##), the browser assumes this information is 1-based. If you submit data in any other format (BED (chr# ## ##) or otherwise), the browser will assume it is 0-based. You can see this both in our liftOver utility and in our search bar, by entering the same numbers in position or BED format and observing the results. Similarly, any data returned by the browser in position format is 1-based, while data returned in BED format is 0-based.</p> <p> For a detailed explanation, please see our blog entry for the <a href="http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/" target="_blank">UCSC Genome Browser coordinate counting systems</a>.</p> <a name="tracks2"></a> -<h2>mRNA associated results</h2> +<h2>mRNA-associated results</h2> <h6>Sometimes when I type in the name of a gene -- e.g. DAO (D aminoacid oxidase) -- the Genome Browser returns a list that includes the gene entry on the assembly, but also contains links to several other genes and aligned mRNAs. What is the relationship between my gene of interest and these results?</h6> <p> The gene search results are obtained from scanning the RefSeq and Known Genes tracks, which are typically based on non-redundant relatively high quality mRNAs. A small fraction of RefSeqs are based on DNA level annotations. In most cases, there is a HUGO Gene Nomenclature Committee symbol or other biological name associated with the gene. In the case of the RefSeq track, the association between these names and the accession is maintained at NCBI and is also present in the refLink table.</p> <p> The mRNA search results are obtained by scanning data associated with the GenBank record for mRNAs. These are often redundant, but occasionally contain something useful that has not yet made it into RefSeq. The mRNA information is often useful because the people who deposited the mRNA into GenBank