Topic

Proteomics
Practicals
Submitted to
Dr.irfan manzoor

Submitted by:
M Mohsin

Roll no:
(6129)

BS. Biochemistry (6th Morning)

Department of Biochemistry
Government College University Faisalabad
 Practical no: 1
How to download genome
“The genome is the entire set of DNA instructions found in a cell”
In humans, the genome consists of 23 pairs of chromosomes located in the cell's nucleus, as well
as a small chromosome in the cell's mitochondria. A genome contains all the information needed
for an individual to develop and function.

Steps to download a genome

1. Open web browser and click on search engine
2. Click on search bar and type www.NCBI.com.

3. Click on national center for biological information.

4. Click on database near search bar and check genome.

5. Click on search bar and write E.coli bacteria.

6. Scroll down to references.

7. Click on Refsek.

8. Click send to and check complete record

9. Also check file.

10. Click on gen bank full and create file.Your file will start downloading.

11. FAASTA is used to get plain DNA sequence.

12. Now you can use this sequence for further study.
 Practical: 2
How to predict gene sequence
Gene prediction refers to process of identifying regions or location of genomic DNA that
encodes gene.the process is necessary to keep up annotation of rapidly increasing sequencing of
genome.The tools for prediction are GeneMarks,GeneMark2,Gene Tack and Easy Gene.

Steps for prediction of gene sequence:

1) Click on google chrome.

2) Search GeneMarks.

3) Click on GeneMark.

4) Copy sequence from previously downloaded file and paste.

5) Click on start GeneMarks.

6) Click on link to generate output data.

7) You can get of any plane DNA sequence by just pasting nucleotide sequence in GeneMarks.
Practical: 3
Translation of given DNA
Translate is a tool which allow translation of DNA sequence into protein sequence.here we will
use EXPASY translate tool.

Steps for translation of DNA sequence:

1. Click on google chrome.

2. Go to ExPASy tools.

3. Click on translate tool.

4. Copy and paste previously downloaded E.coli genome.

5. Click on translate and open reading frame will appear.

6. Click on all downloaded frames and save it.

7. You have got your protein sequence with open reading frames.
 Practical: 4
Characterization of given protein
Protein characterization involves finding out amino acids that makeup the protein,also sequence
of amino acids and their numbers.It plays critical role in determining the safety and efficiency of
biological product.

Steps for characterization of given protein:

1) Open google chrome.

2) Go to ExPASy tool.

3) Click on protoplasm tool.This tool is used for computation of various physical and chemical
parameters of given protein.

4) Copy open reading frame that is solved already and paste it in search box.
5) Click on compute parameters.

6) We can find amino acid sequence,their numbers, isoelectric point,melting point, boiling
point and many more information.

7) Estimated half life and atomic composition can be calculated.

 Practical: 4
Characterization of proteins by PI/MI
Compute pi/MW is a tool which allows the computation of the theoretical pI (isoelectric point)
and MW (molecular weight)

Procedure:
1. Open google chrome.

2. Search ExPASy.

3. Click on ExPASy.

4. Click on compute pi/MW.

5. Click on browse for website.

6. Copy saved open reading frame and paste it in search bar.

7. Click on click here to compute pI/Mw.

 Practical:5
How to find function of unknown protein
BLAST (basic local alignment search tool)is used for finding the sequence of unknown
protein.BLAST finds regions of similarity between biological sequences.The program compares
protein or nucleotide sequence to sequence database and calculate statistical significance.

Steps to find function:

1) Open google chrome.

2) Open NCBI.

3) click on BLAST tool.

4) Click on protein blast.

5) Enter open reading frame.

6) Scroll down.

7) Click on BLAST.Results will appear.

 Practical:6
How to Download Proteome
UNIPORT is unique database to download protein sequence and for its functional analysis.

Steps to download proteome:

1. Open google chrome.

2. Search UNIPROT.

3. Click on UNIPROT.

4. Check on proteome instead of uniportKB.

5. Search for human or any organism of your interest.

6. You can click card or table depending on the form in which data is needed so I clicked table.

7. Scroll down.
8. Click on view proteins.

9. Click on download and check FAASTA format.

10. Proteome will be downloaded.