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Bioinformatics Workshop 2

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The background to today¶s task: HER oncogenes

 Nomenclature: EGFR, HER, erb-b

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Tasks

Download the answersheet (2) documentfrom blackboard

Go to Genbank homepage.http://www.ncbi.nlm.nih.gov/

Search for all the Human EGFR protein

sequences

Remember to select proteins in the drop menu

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EGFR (Homo sapiens):

epidermal growth factor 

receptor 

Click on

Have a look around the site!

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Click on HPRB

FU 228 - 270

REC 361 - 481

FU 496 - 547

FU 552 - 601

REC 57 - 168

TM 646 - 668

Tyr_Kinase 712 - 968

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Go ³Back´

Click on Reference Sequence Details

Click on Swiss Prot P00533

Then click on Fasta

Open the file and copy the sequence

on to your clipboard

Click back and then the NCBI logo

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Click on ³Blast´

³Human´

Database ³RefSeq´

Programme: BlastP

Then Click Away

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Click On ³Select all´ and then

³Distance Tree of Results´

Copy

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Go back to Blast: This time search whole

database (not just human)

(get the sequence from your saved

EGFR FAST A file)

Putative conserved domains have been detected,

click on the image below for detailed results.

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Tasks

Next you will need to go to

http://www.megasoftware.net/mega41.html

When you get the MEGA link, download thewindows version on to your D Drive.

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Launch Mega

Download ³Sequences for class´

from the blackboard site

File > Open Data

Selected ³Sequences for class´

Ignore the Error Message

Utilities > Convert to MEGA format

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Back to MEGA main page

 Alignment >

 AlignmentExplorer Clustal>

Create a new alignment>

Click No for protein>

Then«.

Data>Open>

Retrieve Sequences from file

Click on ³Sequences for class´

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Edit>Select All

 Alignment>Align by CLUST AL

OK to all ³DEFAULT´

File > Exit

Save Data to MEGA file

Open data in MEGA file

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Click Data> Data Explorer 

Display Colour Cells

Highlight ³Conserved Sites´

Download to XL (Excel)

Where are the variable and conservedregions?

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Go back to main MEGA site and click on

Phylogeny

..and play

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Tasks

Looking at the tree diagram, write a

short paragraph explaining what you

think the tree means. You may wish toinclude things such as the basal taxon,

description of who is related to who,

whether there are any major groupingsor clades etc. This section should be no

more than 150 words.

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What is bootstrapping?

Which do you think are the

oncogenic forms?

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Redo the ³alignments´ (on main MEGA

page) but highlighting only the Human

normal and oncogenic forms

What are the conserved and

variable sequences?

How do these relate toprotein motif functions?

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Submission

Send your answer sheet to me by next

week.

Include your Exel spread sheets if you

wish!!