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Using BLAST to Identify Species from Proteins Using BLAST to Identify Species from Proteins

Using BLAST to Identify Species from Proteins - PowerPoint Presentation

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Uploaded On 2018-11-03

Using BLAST to Identify Species from Proteins - PPT Presentation

Adapted from College Boards Investigation 3 Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST What we know so far We already know that DNA can be used to identify animal species at a genetic level ID: 712139

blast species identify sequences species blast sequences identify protein amino step tree evolutionary acid dna phylogenetic relationships sequence proteins

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Slide1

Using BLAST to Identify Species from Proteins

Adapted from College Board’s “Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST”Slide2

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 fossilSlide3

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 Slide4

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?Slide5

What is BLAST?

B L A S T

Basic

Search

Local

Alignment

ToolSlide6

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 speciesSlide7

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 areSlide8

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 genesSlide9

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 relationshipsSlide10

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 hadrosaurSmall 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!Slide11

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 treeSlide12

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 treeSlide13

Step 2

Locate and download the protein fragment files for the fossilized bone specimensSlide14

Step 3

Upload the sequence into BLAST

Go to BLAST homepage:

https://blast.ncbi.nlm.nih.gov/Blast.cgi Click on “Protein BLAST” Slide15

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”Slide16

Step 4

The results page has 2 sections

The first is a graphical display of the matching sequencesSlide17

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 Slide18

Step 4Slide19
Slide20

Now that you have this information...

Follow the PDF instructions for the BLAST search of the fossilized

T. rex

bone amino acid sequenceIf 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