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AP Biology BLAST!
Transcript of AP Biology BLAST!
Yanghwa Hong Primary Question:
Does the cladogram of an unkown specimen based on appearance match the cladogram based on gene sequencing? Background Context: Hypothesis: Abstract Methodology:
1) Devise a hypothesis on where the unknown specimen is placed on the cladogram after observing physical traits of the specimen
2) Download the four gene files off of http://blogging4biology.edublogs.org/2010/08/28/college-board-lab-files/
3) On http://blast.ncbi.nlm.nih.gov/Blast.cgi, upload the files and click BLAST. Fill out the BLAST Data sheet with the Google Data sheet on the gene with the highest max score and lowest e-value (first aligned gene)
4) Rank the importance of each gene and analyze the most closely related species
5) Interpret data and conclude which species are the most closely related to the unknown specimen Results: Conclusion: Work's Cited: Learning Objectives:
To create a cladogram that depicts evolutionary relationships
To analyze biological data with a sophisticated bioinformatics online tool
To use cladograms and bioinformatics tools to ask other questions of your own and to test your ability to apply concepts you know relating to genetics and evolution After the genes of humans and other organisms were sequenced, it is beginning to be possible to find alignments in genes within different organisms. Before this technology, scientists were only able to guess the placement of organisms in the cladogram, a tree-like model of the lineage of several different species, through appearance. However, after the ability to sequence all of the genes, humans now have the ability to confirm or fix cladograms based on geneology. BLAST (Basic Local Alignment Search Tool) can be used to find these connections because it is a database with all of this information. Therefore, through this database, it is now possible to find its placement in the cladogram. Based off of the morphological observations that were made earlier, it can be hypothesized that the unknown specimen is most closely related to birds on the cladogram. Sequence 1:
Protein produced: collagen
Most closely related organism: Gallus gallus (chicken)
Function: Collagen initiates the formation of collagen fibril
Protein produced: shaker
Most closely related organism: Drosophila melanogaster (fruit fly)
Function: the protein is used as a voltage-dependent potassium channel to let potassiumm ions pass
Protein produced: Ubiquitin - Conjugating enzyme
Most closely related organism: Taeniopygia guttata
Function: performs the second step in ubiquitination
Protein produced: Sinesis mitochondrian
Most closely related organism: Alligator sinesis
Function: belongs to the assembly of catalysis Distance Tree Results (in order) Looking at the results, it can be concluded that the unknown specimen is most closely related to birds because the 1st sequence was ranked as the most important, and its closest organism was found to be Gallus gallus, or chicken. The 4th sequence was found to be closest to the alligator; however, since the alligator is very closely related to birds, it can still be applied to birds. The 3rd sequence was found to be closest to zebra finch, showing that the genes were most likely related to birds. The fourth, the least important sequence, was found to relate to Drosophila melanogaster, which was decided to overlook, since it was the least important sequence. Therefore, it was concluded that the unknown specimen's genes belong with the birds in the cladogram. "Ubiquitin-conjugating Enzyme E2Q-like Protein 1 - Mus Musculus (Mouse)." Ubiquitin-conjugating Enzyme E2Q-like Protein 1 - Mus Musculus (Mouse). N.p., n.d. Web. 7 Jan. 2013. <http://www.uniprot.org/uniprot/A0PJN4>.
"Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 7 Jan. 2013. <http://www.ncbi.nlm.nih.gov/pubmed/15383546>.
NCBI. U.S. National Library of Medicine, n.d. Web. 7 Jan. 2013. <http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Dm>. The gene sequence of an unknown specimen was entered into BLAST, where it is possible to find the closest related organism, the function of the gene, and what the distance tree looks like. Through all of this data-collection, it could be used to conclude whether or not the hypothesis based upon appearance was correct regarding the specimen and its place as a branch in the birds. Through all of this data, it was concluded that the unknown specimen with 4 different gene sequences were most closely related to the birds on the cladogram.