UCSC Genome Browser Exercises (tutorial with screenshots)
The Solution includes a selection of solved exercises with captions step by step to illustrate several applications of the UCSC Genome Browser and depending tools, such as BLAT, including a study case over human NR4A2 gene:
1.Locate the gene in the human genome
2. Hide all tracks and display the RefSeq gene (compact)in the genome browser
3. Indicate the coordinates of the gene in the genome
4. Is the gene transcribed in the main strand or in the complementary strand?
5. Obtain main infomation and links of human NR4A2 gene (OMIM, PubMed)
6. Download the gene sequence, with the introns in lower case and the exons in upper case
7. Extract the promoter region of the gene (1500 bases upstream)
8. Download the sequence of the predicted protein
9. Display all SNPs in NR4A2 gene.
10.Use BLAT to align NR4A2 gene to the mouse genome, in order to obtain the corresponding orthologous gene. Indicate the coordinates of the orthologous gene in the mouse genome
11. Add a custom track for NR4A2 gene in UCSC Genome Browser. Color the track in pink.