1 / 20

Using BLAST to Identify Species from Proteins

Explore the application of BLAST in comparing amino acid sequences to identify evolutionary relationships between extinct and modern species. Learn how to create phylogenetic trees to understand genetic relatedness. Follow step-by-step instructions to analyze fossilized bone specimens using BLAST.

bellc
Download Presentation

Using BLAST to Identify Species from Proteins

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Using BLAST to Identify Species from Proteins Adapted from College Board’s “Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST”

  2. What we know so far... • We already know that DNA can be used to identify animal species at a genetic level • According to the Central Dogma of Biology, DNA is transcribed into RNA and translated into proteins • If DNA is not present in a bone specimen, other biological material can be acquired to identify a fossil

  3. Today’s Goal • Become acquainted with BLAST for protein analysis • Identify the relation of extinct dinosaurs to modern species and where dinosaurs fit in on a family tree • Understand how phylogenetic trees depict evolutionary relationships

  4. What you will need to know • What is BLAST, and how is it used? • Why is BLAST important? • What is a phylogenetic tree? • What are orthologs? • How can proteins be used to identify evolutionary relationships?

  5. What is BLAST? B L A S T Basic Local Alignment Search Tool

  6. Why is BLAST useful? • BLAST makes it easy to search databases that contain many millions of partial, full, and potential gene sequences • It can be used to compare sequences from one species to another to identify similarities or differences • Knowing the identity of gene sequences from many species allows scientists to track evolutionary heritage of those species

  7. What is a phylogenetic tree? • Diagram that depicts the evolutionary relatedness of species or groups of closely related species • Each endpoint of a branch represents a group of organisms • The closer two branches on a tree are, the more related the groups are

  8. What are orthologs? • Orthologs are genes in different species that evolved from a common ancestral gene • Basically, they are genes with the same or similar functions in different species • Ex. Human and mouse genes

  9. How can proteins be used to identify genetic relationships? • Proteins are composed of different combinations of amino acids • The genetic code (DNA/RNA) is used to identify each amino acid to then add on to a growing chain (protein) • There are 20 amino acids and 64 possible combinations of RNA building blocks- some amino acids are repeated! • We can examine differences in protein sequences between species to infer evolutionary relationships

  10. Activity: Identify Evolutionarily Related Protein Sequences • You are a member of a scientific team that has discovered 3 well preserved bone fossil specimens • T. rex, mastodon, and hadrosaur • Small amounts of tissue have been removed from the fossil • Unusual in such ancient specimens • Amino acid sequences have been extracted from protein fragments • First time this has ever happened!

  11. Activity: Identify Evolutionarily Related Protein Sequences • Use BLAST to compare these amino acid sequences to protein sequences from other species • Then, create a phylogenetic tree to explore where these extinct species might branch off from the evolutionary tree

  12. Step 1 • Form an initial hypothesis as to where and why you think the three extinct species (T. rex, hadrosaur, mastodon) belong on the phylogenetic tree

  13. Step 2 • Locate and download the protein fragment files for the fossilized bone specimens

  14. Step 3 • Upload the sequence into BLAST • Go to BLAST homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi • Click on “Protein BLAST”

  15. Step 3 • Under “Enter Query Sequence,” paste the first amino acid sequence from “Protein #1” • Do not change any of the settings on the rest of the page • Scroll down and hit “BLAST”

  16. Step 4 • The results page has 2 sections • The first is a graphical display of the matching sequences

  17. Step 4 • Scroll down to the section titled “Sequences Producing Significant Alignment” • The species in this list are the ones with sequences identical to or most similar to the amino acid sequence of interest • The most similar sequence is listed first • If you click on a result listed, you will get a full report of the species

  18. Step 4

  19. Now that you have this information... • Follow the PDF instructions for the BLAST search of the fossilized T. rex bone amino acid sequence • If you still have time at the end of class and want to practice and explore more, repeat the activity for the hadrosaur and mastodon fossil specimens

More Related