Comparing DNA Sequences to Understand Evolutionary Relationships With Blast

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, you’ll 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, you’ll 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.