Notes on USCS genome broswer

ucsc genome browsers

https://users.soe.ucsc.edu/~kuhn/workshops/spelman2015/


variant annotation integrator
assembly data hubs
100way multiple alignment on human
virtual machine (a local ucsc browser, GBIB genome browser in a box. A standalone version, and can be downloaded.)
youtube training channel

MySQL in the backend
Sequence files are stored separately.

plant hub using ‘track data hubs’  (upload tracks for references genomes in UCSC).

xeno RNA
http://en.wikipedia.org/wiki/Xeno_nucleic_acid


“My Data”, -> “Session”  for shared project views.


GenomeWiki


BED4 format for tracks
 https://genome.ucsc.edu/FAQ/FAQformat.html

**Download sessions locally. Session will expire after 3-4 months.

exercises for ucsc genome browswer

http://www.explorebiology.com/apbiology/labs/

https://cbse.soe.ucsc.edu/news/article/1915

https://courses.soe.ucsc.edu/courses/bme200/Fall12/01


http://blog.openhelix.eu/?p=17616

How to zoom-in on selected coordinates in UCSC genome browser

To zoom in on a selected region, we can high-light a region and then select zoom-in.

Alternatively, we can type the chromosome number and coordinates into the search window:

In this example, we see introns

The dashed line of MSH2 locus indicate introns.



The blocks in this picture are exons with coding regions,

In the following picture, the circled regions are 5' untranslated regions, i.e., 5'UTR, because this region is at the 5' end of "ATG". Notice that 5'UTR is also in an exon.