1. Use the six Sequences to run Multi-LAGAN
(http://lagan.stanford.edu/lagan_web/index.shtml). Enter sequences, enter in the
species names down below, and then submit.
a. Draw out a rough sketch or screenshot of the tree (use organism names)
b. Open the VISTA Browser link for chimp. Which species has
by far the longest conservation with chimp?
Humans have the longest conservation with chimps
c. Which species has the least conservation with chimp?
Zebrafish have the least amount of conservation with chimp.
d. Run a Clustal-W2 alignment of the DNAs ( ).
Copy and paste here CLUSTAK guide tree. Does the tree agree with the
LAGAN tree?
The trees agree in some parts but
differ in many other parts.

2. Using the sequences with gi numbers 513174699 and 345782223 ( or,
XM_003640935.2 and XM_540154 respectively) , run pairwise LAGAN, which can
be found at http://lagan.stanford.edu/lagan_web/index.shtml. Click the Vista Point
link for 345782223.
a. Give the approximate nucleotide positions of an exon?
b. Under Tools, click the CNS link. Where are the reported conserved regions?
c. What is the listed percent identity in those regions?
d. Why is there no phylogenetic tree produced by pairwise-LAGAN?
3. Retrieve the problem 3 cow sequence from Blackboard. Run a BLAT search
(http://genome.ucsc.edu/cgi-bin/hgBlat) of the human genome (Feb. 2009).
a. What is the percent identity of the match with the longest span?
The percent identity is 89.9%.
b. Click the browser link for that hit. What is the chromosomal location?
It is located on chromosome 11.
c. What is the gene name under RefSeq Genes (you may have to click to the left
to expand the RefSeq region)?
The gene is CSRP3.
d. Set the Flagged SNPs track to pack. How many SNPs in this region are
flagged as having a clinical association?
There are a total of 27 flagged clinical association.
e. How many of those are non-synonymous SNPs (red)?
There are a total of 22 non-synonymous SNPs
f. What is a non-synonymous SNP?
Non-synonymous SNP are changes that change the sequence in the protein.
g. Turn the Genscan Genes track to full. Are there any genes predicted in this
region?
There is a gene in the predicted region.
h. How well does the pattern of exons from Genscan match the actual exons?
The exons match almost exactly with the Genscan gene except for two exon.This study source was downloaded by 100000817883310 from CourseHero.com on 05-12-2022 12:07:13 GMT -05:00
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