Lab 3: UCSC Browser and BLAST
1. Learn to access information from UCSC.
BLAST: Basic Local Alignment Search Tool. BLAST is a search algorithm based on local
alignment, designed to quickly find sequences similar to the query sequence in a large
database.
UCSC is a bioinformatics tool developed by the University of California, Santa Cruz
(UCSC) for visualizing and analyzing genomic data.
Example: Hemoglobin is a tetramer composed primarily of two alpha globin subunits
and two beta globin subunits. Consider alpha-globin. There are two related human
genes (official gene symbols HBA1 and HBA2). Use the UCSC Genome Browser (http://
genome.ucsc.edu/ ) to determine the length of the intergenic region between the HBA1
and HBA2 genes.
You have two options: (1) Get an approximate answer using Genome Browser
(2) Get a more precise answer using the Table Browser
Option 1: You can get an approximate answer visually:
Go to the UCSC website(http://genome.ucsc.edu/), and choose Genome Browser by
clicking the mouse.
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Next, enter Human, HBA1, choose assembly GRCh38 in the UCSC Genome Browser,
and press “GO”
Then, Select RefSeq Genes: HBA1 - chr16:176680-177522 - (NM_000558) hemoglobin
subunit alpha
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Then, Zoom out 10-fold and you will see the adjacent HBA1 and HBA2 genes:
You can drag (hold your cursor just below the ideogram) and select the region
between HBA2 and HBA1 shown below to find that the distance is about
______________ base pairs.
Option2: To get a more precise answer use the Table Browser http://genome.ucsc.edu/
cgi-bin/hgTables
Or choose Table Browser from the Tools menu:
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Set a region encompassing both genes and set the various menus as shown here:
This is the output (set to all fields)
You may choose the output format as BED-browser extensible data:
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This is the output (as a BED file). From either of these outputs, you can calculate the
exact intergenic distance.
BED format explanation is here: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
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Take the beginning of the HBA1 (NM_000558) gene’s position_176716______and
subtract the end of the HBA2 (NM_000517) gene’s position___173600___. So the
length of the intergenic region between the HBA1 and HBA2 genes
=__176716-173600= 3116_____
2. Accessing information from the UCSC Table Browser (http://genome.ucsc.edu/ )
How many single nucleotide polymorphisms (SNPs) span the human beta-globin gene?
(1) Start at the HBB region of the UCSC Genome Browser and click the “Table Browser”
in the “Tools” menu. Alternatively, you can go to the UCSC website (http://
genome.ucsc.edu) and click the “Table Browser” tab. Set the clade to Mammal,
genome to Human, assembly to GRCh38/hg38, group to Variation, track to
dbSNP153, table to All dbSNP(153) (dbSnp153), and region to position
chr11:5225464-5227071. Note that if the position is not already set, you can type
hbb into the position box, click “lookup,” and the correct position will be entered.
(2) To see the answer to this problem, click “summary/statistics.” The item count tells
you how many SNPs there are. What’s the number? 978
(3) To see the answer as a table, set the output format to “all fields from the selected
table,” make sure the “Send output to Galaxy / GREAT” boxes are not checked, and
click the “get output” box. The SNPs are shown as a table including chromosome,
start, and stop position.
(4) Try the various output options, such as a bed file or a custom track. Note that you
can output the information as a file saved to your computer.
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3. Protein searches are usually more informative than DNA searches. Do a BLASTP
search using RBP4 (NP_006735), restricting the Database to nr and Organism to
Arthropoda (taxid:6656) (insects).
https://blast.ncbi.nlm.nih.gov/Blast.cgi?
PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
Click BLAST
How many matches have an E value less than 1e-07?
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