Blast LAB
BLAST Lab Assignment
A team of scientists having discovered a fossil specimen near Liaoning Province, China. Our goal is to observe the physical structure of this fossil and determine the most likely placement of the fossil species in a cladogram. After careful examination of the fossil we notice some traits that could assist us in the classification of the species. For instance, it seems to have a vertebrae and what seems to be wing like extensions from its body. We therefore form the hypothesis that the gene of interest might belong to the bird group of the cladogram. To aid us in the classification we are given the gene sequence of 3 other species in which share similarities with the gene of interest:
Gene #1: gallus gallus collagen, Type V alpha (Bird), anas platyrhyncas, e=0.0.
Gene #2: drasophila melanogaster shaker(sh), haematobia irritans exigua 95% similarity, e=0.0.
Gene #3: Taeniopyqia guttata (zebrae finch), geospiza fortis 99% medium ground finch, e=0.0.
Methods:
1- Make an initial hypothesis as to where this specimen might likely be placed on the cladogram.
2- Gather information on 3 gene types to assist us in classifying this fossil.
3- Study and compare the gene sequence of the 3 genes with the gene of interest using BLAST website.
4- Click on the link titles “Distance Tree Results” and study the cladogram given of each species and which group it is place in.
Results: We realize that our hypothesis is correct and that the most similar gene to the gene of interest is gene #3 (taeniopyqia guttata). Gene#3 belongs in the birds group of the cladogram, and therefore the gene of interest is of that same group.
Answers to Questions page#S48:
1. The results obtained from BLAST inform us that gene #3 has the most similar gene sequence to the gene of the specimen found in the fossil.
2. The species is located on the birds branch of the given cladogram.
3. The gene sequence was 100% similar to the gene of interest.
4.
A team of scientists having discovered a fossil specimen near Liaoning Province, China. Our goal is to observe the physical structure of this fossil and determine the most likely placement of the fossil species in a cladogram. After careful examination of the fossil we notice some traits that could assist us in the classification of the species. For instance, it seems to have a vertebrae and what seems to be wing like extensions from its body. We therefore form the hypothesis that the gene of interest might belong to the bird group of the cladogram. To aid us in the classification we are given the gene sequence of 3 other species in which share similarities with the gene of interest:
Gene #1: gallus gallus collagen, Type V alpha (Bird), anas platyrhyncas, e=0.0.
Gene #2: drasophila melanogaster shaker(sh), haematobia irritans exigua 95% similarity, e=0.0.
Gene #3: Taeniopyqia guttata (zebrae finch), geospiza fortis 99% medium ground finch, e=0.0.
Methods:
1- Make an initial hypothesis as to where this specimen might likely be placed on the cladogram.
2- Gather information on 3 gene types to assist us in classifying this fossil.
3- Study and compare the gene sequence of the 3 genes with the gene of interest using BLAST website.
4- Click on the link titles “Distance Tree Results” and study the cladogram given of each species and which group it is place in.
Results: We realize that our hypothesis is correct and that the most similar gene to the gene of interest is gene #3 (taeniopyqia guttata). Gene#3 belongs in the birds group of the cladogram, and therefore the gene of interest is of that same group.
Answers to Questions page#S48:
1. The results obtained from BLAST inform us that gene #3 has the most similar gene sequence to the gene of the specimen found in the fossil.
2. The species is located on the birds branch of the given cladogram.
3. The gene sequence was 100% similar to the gene of interest.
4.