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Practical

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109 views9 pages

Practical

Uploaded by

mairabilal78
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Practical No.

01: Overview of NCBI Database


Introduction:
The National Center for Biotechnology Information (NCBI) is part of the United States
National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is
approved and funded by the government of the United States. The NCBI is located in Bethesda,
Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude
Pepper.
The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an
important resource for bioinformatics tools and services. Major databases include GenBank for
DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases
include the NCBI Epigenomics database. All these databases are available online through
the Entrez search engine. NCBI was directed by David Lipman, one of the original authors of
the BLAST sequence alignment program and a widely respected figure in bioinformatics.
Website Url: https://www.ncbi.nlm.nih.gov/
Username: [email protected]
Password: Naveed94210.

Practical No.02: Searching & Retrieval of Data from NCBI.


Objective
To learn how to search and retrieve biological data using accession numbers from the National
Center for Biotechnology Information (NCBI) database.

Materials
- Computer with internet access
- Web browser
- NCBI account (optional)

Introduction
The NCBI provides a wealth of biological data, including DNA, RNA, and protein sequences.
Each entry in the NCBI database is assigned a unique accession number. This practical will
guide you through searching for and retrieving data using these accession numbers.

Procedure
Step 1: Accessing the NCBI Website

 Open your web browser.


 Go to the NCBI homepage at https://www.ncbi.nlm.nih.gov
Step 2: Searching Using an Accession Number

 On the NCBI homepage, locate the search bar at the top of the page.
 Enter the accession number (for example, `AH002765.2` for a Nucleotide sequence) into
the search bar.
 Click the search icon or press Enter.
Step 3: Understanding the Search Results

 The search results page will display information about the accession number entered.
 Look for the relevant entry, which will usually be the first result. This entry will contain
links to various databases like GenBank, RefSeq, and others.
Step 4: Accessing Detailed Information

 Click on the entry link to access the detailed view.


 In the detailed view, you will find multiple tabs, such as "GenBank," "FASTA,"
"Graphics," and "Analyze this sequence."
 Click on FASTA: This shows the sequence in FASTA format
Step 5: Downloading Data

 To download the sequence data, go to the "Send to" button located at the top right of the
detailed view page.
 Select the desired format (e.g., FASTA, GenBank) from the dropdown menu.
 Click on the "Create File" button to download the data to your computer.

Step 6: Using NCBI Tools for Further Analysis

 Explore the "Analyze this sequence" and click on Run BLAST for further analysis.
 BLAST (Basic Local Alignment Search Tool) allows you to compare your sequence with
other sequences in the database to find regions of similarity.

Practical No.03: Searching & Retrieval of Data from UNIPROT.


Objective
To learn how to search and retrieve protein data from the UniProt database using accession
numbers.
Materials Required
- Computer with internet access
- Web browser

Introduction
UniProt (Universal Protein Resource) is a comprehensive, high-quality, and freely accessible
database of protein sequence and functional information. Each protein entry in UniProt is
assigned a unique accession number which can be used to retrieve detailed information about the
protein.

Procedure
Step 1: Access the UniProt Website
1. Open your preferred web browser.
2. Navigate to the UniProt website: https://www.uniprot.org/

Step 2: Understand the UniProt Interface


Familiarize yourself with the main sections of the UniProt homepage.
 Search Bar: For querying the database using various parameters including accession
numbers.
 Tools and Services: Additional tools provided by UniProt for data analysis.
 Help: Documentation and tutorials to assist users.

Step 3: Retrieve Data Using Accession Number

 Write the accession number `P05067` in the search bar and enter.
 The search results will display the protein entry associated with the accession number.

Step 4: Downloading Data


1. Click on the `Download` button located at the top right corner of the entry page and select the
desired format.
2. Download data in FASTA (canonical) format.
Step 5: Using Additional Tools and Resources
1. Then run BLAST: For sequence alignment and similarity searches.

Practical No.04: Searching & Retrieval of Data from BLAST N


(Nucleotide)
Practical No. 02
1. After Run BLAST
2. Select BLAST N:
- On the BLAST homepage, click on the "Nucleotide BLAST" link under the "Basic BLAST"
section. This will take you to the BLASTN search page.
3. Locate the Search Box for Accession Number:
- On the BLASTN search page, locate the search box where you can enter the nucleotide
sequence, accession number, or other identifiers.
4. Enter the Accession Number:
- In the search box, enter the accession number of the nucleotide sequence you want to retrieve.
For example, enter "NM_001301717" (you can use any valid accession number for your search).

5. Set the Parameters (Optional):


- You can set various parameters for your BLAST search, such as the database to search against
(e.g., "nr" for non-redundant nucleotide sequences), algorithm parameters, and filters. Write the
organism’s name of the given accession number and enter.

 To check in the same organism  Not Exclude.


 To check in different organisms  Exclude

I didn’t select to Exclude the Homo sapiens. It means I’m checking in the same organisms.
6. Execute the BLAST Search:
- Scroll down to the bottom of the page and click the "BLAST" button to initiate the search.
The search might take a few moments to complete.

7. Review the Results:


Once the search is complete, you will be directed to the results page. The results page shows a
graphical summary, descriptions of the hits, alignments, and a link to the original nucleotide
sequence.

8. Retrieve the Nucleotide Sequence Data:


- In the "Descriptions" section, select the entry that is most highly similar to the accession
number you entered. Click on the accession number link to view detailed information about the
nucleotide sequence.

- This will take you to the NCBI nucleotide database page for that sequence. Here, you can see
the complete nucleotide sequence, as well as additional information such as the gene name,
organism, and related sequences. I selected the 1st highest similar entry

9. Results of the Retrieved Data:


Write the results by noting down the following details:
Query length  20535
Accession Number  AH002765.2
Gene Name  Homo sapiens retinoblastoma susceptibility protein gene
Organism  Homo sapiens
Bits Score  4340 (Exact Score 2350)
Number of Matches  23
E value  0.0
Identities  100%
Gaps  0%

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