Oct 12, 2020
Protocol to UCSC Genome Browser & BLAST
Forked from Protocols for Bioinformatic Tools
This protocol is a draft, published without a DOI.
- 1UCSC
- UCSC BME 22L
Protocol Citation: Ikenna Anigbogu 2020. Protocol to UCSC Genome Browser & BLAST . protocols.io https://protocols.io/view/protocol-to-ucsc-genome-browser-amp-blast-bnc3mayn
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: October 12, 2020
Last Modified: October 12, 2020
Protocol Integer ID: 43131
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Abstract
In this lab, students will work through BLAST and the UCSC Genome browser to find and analyze information about their genes of interest.
UCSC Genome Browser
UCSC Genome Browser
Genome Browser
You will now have the opportunity to utilize these tools yourself to investigate a gene that you find interesting. Use these tools to answer the questions below and then relay these in the Lab Results of this Lab Notebook.
Find a gene of interest and type it onto the genome browser. Use the human GRCh37/hg19 Assembly. In your own words, give a brief description of this gene’s function.
Look through the tracks given on the displays and give the name of track which is used to give gene expression for different tissue types. What tissue do we observe the highest expression of RNA? (use track other than NCBI RefSeq)
What orthologs does this gene have? What is the significance of having these as an ortholog?
What Biochemical and Signaling Pathways is this gene involved in? Again, what is the signficance?
What diseases are associated with this gene?
BLAST
BLAST
BLAST
Do a BLAST search of a gene of interest.
Look at the BLAST results. Give the:
- Top 5 scores
- Top 5 species this gene is found in
- Lowest E-Value (if any)