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Zara Vimawala

Lab ap bio

Comparing DNA Sequences to Understand Evolutionary
Relationships with Blast
Introduction/Purpose: All species have a common ancestry and can be classified.
Cladograms are diagrams that depict the evolutionary relationships between organisms.
The purpose of this activity is to create a cladogram, depict evolutionary relationships
among different species, and relate genetics to evolution. In this activity, bioinformatics
will be used to analyze similarities and differences in gene sequences between different
species. Bioinformatics is a field that combines statistics, mathematical modeling, and
computer science to analyze biological data. The last gene of interest that I chose to study
was sickle cell anemia.
Materials
Pencil and paper
Computer with access to
http://blogging4biology.edublogs.org/2010/08/28/college-board-lab-files/.
http://blast.ncbi.nlm.nih.gov/Blast.cgi
4. Procedure
Form an initial hypothesis as to where you believe the fossil specimen should be placed
on the cladogram based on the morphological observations you made earlier. Draw your
hypothesis on Figure 4.
Locate and download gene files. Download three gene files from
http://blogging4biology.edublogs.org/2010/08/28/college-board-lab-files/.
Upload the gene sequence into BLAST by doing the following:
a. Go to the BLAST homepage: http://blast.ncbi.nlm.nih.gov/Blast.cgi
b. Click on Saved Strategies from the menu at the top of the page.
c. Under Upload Search Strategy, click on Browse and locate one of the gene files
you saved onto your computer.
d. Click View.
e. A screen will appear with the parameters for your query already configured. NOTE:
Do not alter any of the parameters. Scroll down the page and click on the BLAST
button at the bottom.
Zara Vimawala
Lab ap bio

After collecting and analyzing all of the data for that particular gene (see instructions
below), repeat this procedure for the other two gene sequences.
The results page has two sections. The first section is a graphical display of the matching
sequences.
Scroll down to the section titled Sequences producing significant alignments. The
species in the list that appears below this section are those with sequences identical to or
most similar to the gene of interest. The most similar sequences are listed first, and as you
move down the list, the sequences become less similar to your gene of interest.
If you click on a particular species listed, youll get a full report that includes the
classification scheme of the species, the research journal in which the gene was first
reported, and the sequence of bases that appear to align with your gene of interest.
If you click on a particular species listed, youll get a full report that includes the species
classification scheme, the research journal in which the gene was first reported, and the
sequence of bases that appear to align with your gene of interest.
If you click on the link titled Distance tree of results, you will see a cladogram with the
species with similar sequences to your gene of interest placed on the cladogram
according to how closely their matched gene aligns with your gene of interest.
5. Results/Analysis
Gene 1
1. The species in the BLAST results that has the most similar gene sequence to the
gene of interest is Gallus gallus collagen.
2. The species is located near the birds on the cladogram.
3. The gene sequence is a 100% match.
4. The Meleagris gallopavo colaagen is the next most similar species to the gene of
interest.
Gene 2
1. The species in the BLAST results that has the most similar gene sequence to the
gene of interest is Drosophilia melanogaster.
2. The species is located near the insects on the cladogram.
3. The gene sequence is a 99% match.
4. The Drosophilia pseudoobscura is the next most similar species to the gene of
interest.
Gene 3
1. The species in the BLAST results that has the most similar gene sequence to the
gene of interest is Taeniopyqia guttata.
Zara Vimawala
Lab ap bio

2. The species is located near the birds on the cladogram.
3. The gene sequence is a 100% match.
4. The Taeniopyqia guttata clone and Meleagris Gallopavo are the next most similar
species to the gene of interest.
Design and Conduct Your Own Experiment: Keratin
1) Keratin is key structural material making up the outer layer of the human skin. It
is also structural material for the hair and nails. It provides strength and resilience
to skin and protects the skin from damage.
2) It is most likely to be found in primates, mice/rats, and mammals in general.
3) Yes, it is possible to find the same gene in two different kinds of organisms.
There are several variations of skin such as skin on humans and scales on reptiles.
4) It suggests that organisms have a common ancestor and that the gene existed
earlier in the evolutionary tree.
5) Other characteristics are still important in studies. Keratin I similarities show only
part of the relationship.
Conclusion:
In conclusion, the relationship between species can be proved through gene sequences
and can be represented through cladograms. Gene one and three were closely related to
birds. Gene two was closely related to insects. The gene for keratin was closely related to
Homo sapiens. Using bioinformatics concluded the similarities and differences between
gene sequences of different species. Identification of these similarities, differences, and
entire gene sequences can enable us to better understand genetic diseases and prevent
these diseases. This information can also be used to understand the closeness of the
ancestry between organisms. These single genes contribute to the entire genome of
species. This allows people to make hypotheses and formulate conclusions about entire
genomes.

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