comparing dna sequences to understand evolutionary relationships with blast
DESCRIPTION
Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST. INVESTIGATION 3 BIG IDEA 1. Tutorials for BLAST at NCBI. The NCBI Handbook. BLAST H ome P age. Student Investigation. Getting Started (pages S43 & S44) - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/1.jpg)
Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST
INVESTIGATION 3BIG IDEA 1
![Page 2: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/2.jpg)
Tutorials for BLAST at NCBI
![Page 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/3.jpg)
The NCBI Handbook
![Page 5: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/5.jpg)
Student Investigation
• Getting Started (pages S43 & S44)– Table 1: students construct a cladogram of the
major plant groups.
– Table 2: students construct a cladogram depicting evolutionary relationships among 5 species according to percent similarity.
![Page 6: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/6.jpg)
Student Investigation
• Team of scientists uncovered this fossil specimen in China.
• Students make general observations about morphology and record those in lab notebook. (Page S44)http://www.pbs.org/wgbh/nova/microraptor/foss-09.html
![Page 7: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/7.jpg)
Student Investigation• Procedure (page S45)– STEP 1: Students form initial hypothesis as where
they think the fossil specimen should be placed on the cladogram based on morphological observations made earlier.
– Task is to use BLAST to determine most likely placement of fossil species in a cladogram
– Based on DNA sequences extracted from tissue
![Page 8: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/8.jpg)
Student Investigation
• Procedure (page S45)• STEP 2: Students locate and download 3 gene
files from Using Blogs In Science Education site.
• http://blogging4biology.edublogs.org/2010/08/28/college-board-lab-files/
• Remind students that they cannot open files, but must upload to BLAST to view sequences.
![Page 9: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/9.jpg)
Student Investigation
• STEP 3: Students upload first gene sequence into BLAST by going to BLAST home page and clicking on “Saved Strategies” from menu at top of page.
![Page 10: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/10.jpg)
BLAST Home Page
![Page 11: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/11.jpg)
Uploading Gene Sequences
Click on “View” and upload a gene sequence. You cannot view the file on your computer.
![Page 12: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/12.jpg)
Click on BLAST
Click on BLAST button at the bottom of the page.
![Page 13: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/13.jpg)
ResultsClick on a particular species to find out more specific information, including the classification scheme and the sequence of bases that appear to align with your gene of interest.
![Page 14: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/14.jpg)
ResultsClick on a particular species to find out more specific information, including the classification scheme and the sequence of bases that appear to align with your gene of interest.
![Page 15: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/15.jpg)
Distance Tree of Results
![Page 16: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/16.jpg)
The Cladogram
![Page 17: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/17.jpg)
The Cladogram
This is a close-up of what you will see. Your gene of interest is highlighted in yellow.
![Page 18: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/18.jpg)
The Cladogram
In addition, you will be provided with a “BLAST names color map” that looks like this so that you can better understand the cladogram your search produced.
![Page 19: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/19.jpg)
What’s next?
• Students will– Repeat this process for 2 other genes of interest.– Analyze their results.– Decide whether or not the data from the BLAST
search support their hypothesis about the placement of the fossil species on the cladogram.
– Compare and discuss cladogram with other students.
![Page 20: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/20.jpg)
Design and Conduct Investigation
• Students will– Find and BLAST their own genes of interest.– Use example procedure provided.– Possibly use one or more of the suggested genes
to explore.OR – use another source like SWAMI or ENSI before or
after doing this lab.
![Page 21: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/21.jpg)
SWAMI
![Page 22: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/22.jpg)
SWAMI
![Page 23: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/23.jpg)
ENSI
![Page 24: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST](https://reader035.vdocument.in/reader035/viewer/2022062812/56816353550346895dd3f572/html5/thumbnails/24.jpg)