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Bioinformatics Module.docx

This document is a certificate for students of T.Y.B.Sc. Microbiology at Jai Hind College, confirming the completion of Bioinformatics practicals during the Sixth Semester of the academic year 2024-2025. It includes detailed steps for various bioinformatics tasks such as multiple alignment of protein sequences, pairwise alignment, conserved domain search, six-frame translation, restriction analysis, and phylogenetic tree construction. Additional resources for further learning are also provided.

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Vallabhi Sheth
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© © All Rights Reserved
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Download as PDF, TXT or read online on Scribd
1 views

Bioinformatics Module.docx

This document is a certificate for students of T.Y.B.Sc. Microbiology at Jai Hind College, confirming the completion of Bioinformatics practicals during the Sixth Semester of the academic year 2024-2025. It includes detailed steps for various bioinformatics tasks such as multiple alignment of protein sequences, pairwise alignment, conserved domain search, six-frame translation, restriction analysis, and phylogenetic tree construction. Additional resources for further learning are also provided.

Uploaded by

Vallabhi Sheth
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Jai Hind College,

Autonomous

Certificate
SIXTH SEMESTER

This is to certify that Mr. /Ms. _______________________________________

of T.Y.B.Sc. Microbiology has satisfactorily completed the Bioinformatics

practicals as prescribed by the Jai Hind College during the Sixth Semester of

the academic year 2024 -2025

Signature of the Staff Incharge​ ​ Signature of Head of the Dept.

Signature of the Examiner​ ​ ​ ​ Date and College Stamp


VISIT HOMEPAGES- NCBI, EMBL, DDBJ, PIR, PDP, KEGG

Steps:

1)​ Go to google homepage.


2)​ Type the databases above and visit the homepage.
3)​ Note down all the available tools and services provided
MULTIPLE ALIGNMENT OF PROTEIN SEQUENCE USING BLASTP

Steps:

1)​ Go to NCBI site. Go to popular resources and select ‘PROTEIN’.


2)​ In the search field, enter the protein of your choice. Eg. Beta-galactosidase in E.coli
3)​ A dropdown list will appear. Select one name or gene ID of your interest from the list
4)​ When the new page opens select FASTA format or accession number, highlight and copy the
entire text.
5)​ Go to protein BLAST.
6)​ Enter the sequence in FASTA format or accession number as query. For larger sequence
select the query subrange
7)​ Choose nr database.
8)​ Click on the BLAST and observe the results, see graphical summary, dot matrix view,
descriptions and alignment
PAIRWISE ALIGNMENT OF PROTEIN SEQUENCE USING BLASTP

Steps:

1)​ Go to NCBI site. Go to popular resources and select ‘PROTEIN’.


2)​ In the search field, enter the protein of your choice. Eg. Beta-galactosidase in E.coli
3)​ A dropdown list will appear. Select one name or gene ID of your interest from the list
4)​ When the new page opens select FASTA format or accession number, highlight and copy the
entire text.
5)​ Go to NCBI site and select another protein with which you wish to perform pairwise
alignment. Eg. Beta-galactosidase in K.pneumoniae
6)​ Highlight and copy the FASTA format or accession number
7)​ Go to protein BLAST.
8)​ For pairwise align check on the option- Align two or more sequences.
9)​ Enter both the data in the query and subject sequence section.
10)​Click on the BLAST and observe the results, see graphical summary, dot matrix view,
descriptions and alignment

NOTE:For Alignment of nucleotide sequence use BLASTN program.


FISHING OUT SEQUENCE HOMOLOGY- CONSERVED DOMAIN SEARCH

Steps:

1)​ Go to NCBI site.


2)​ In the ANALYZE section, select the tool Conserved Domain Search Service (CD Search)
3)​ In the search field, enter the protein of your choice. Eg. Beta-galactosidase in E.coli and
submit
4)​ For multiple sequence study, select BATCH CD and submit the data for analysis
5)​ A dropdown list will appear. Select one name from the list
6)​ Observe the results and note the similarities
7)​ You can also search for proteins with similar domain architecture

NOTE: MULTIPLE ALIGNMENT OF PROTEINS AND NUCLEOTIDE SEQUENCES ALONG WITH


CONSERVED DOMAIN SEARCH CAN ALSO BE CARRIED OUT USING CLUSTAL W
SIX FRAME TRANSLATION OF GIVEN NUCLEOTIDE SEQUENCE

Steps:

1)​ Go to NCBI site.


2)​ Go to popular resources and select ‘NUCLEOTIDE’.
3)​ In the search field, enter the NUCLEOTIDE of your choice. Eg. Genome of E.coli
4)​ A dropdown list will appear. Select one name or gene ID of your interest from the list
5)​ When the new page opens select FASTA or accession number, highlight and copy the entire
text.
6)​ Go to NCBI homepage
7)​ In the ANALYZE section, select the tool Open Reading Frame Finder (ORF Finder)
8)​ Paste the FASTA sequence in the text box. In search parameters change the minimal ORF
length to 75
9)​ Scroll down and Click on Submit and observe the results
10)​A dropdown list will display all possible ORF considering six frame translation.
11)​Select an ORF with maximum nucleotide length and negative sense (template strand).
12)​Translated sequence of amino acids will be displayed in the side panel.
13)​To identify the protein product, click on the BLAST option and study the results displayed
RESTRICTION ANALYSIS OF NUCLEOTIDE SEQUENCE

Steps:

1)​ Go to NCBI site.


2)​ Go to popular resources and select ‘NUCLEOTIDE’.
3)​ In the search field, enter the NUCLEOTIDE of your choice. Eg. Genome of E.coli
4)​ A dropdown list will appear. Select one name or gene ID of your interest from the list
5)​ When the new page opens select FASTA or accession number, highlight and copy the entire
text.
6)​ Open Google on a new tab and enter RESTRICTION MAPPER
7)​ Paste the FASTA sequence in the text box.
8)​ In sort by parameters select all enzymes
9)​ Click on Map sites and observe the results
CONSTRUCTION OF PHYLOGENETIC TREE

Steps:

1)​ Go to NCBI site.


2)​ Go to popular resources and select ‘PROTEIN’.
3)​ In the search field, enter the protein of your choice. A dropdown list will appear. Select one
name or gene ID of your interest from the list
4)​ When the new page opens select FASTA or accession number, highlight and copy the entire
text.
5)​ Retrieve the same protein sequence from different organisms.
6)​ Go to NCBI homepage
7)​ In the ANALYZE section, select the tool COBALT(Constraint based multiple alignment tools).
8)​ Submit the sequence from various organisms
9)​ Analyze the data, click on the phylogenetic tree for tree construction.
10)​Alternatively, you can Choose CLUSTAL W. The phylogenetic tree is displayed only if the
system is JAVA enabled.

Additional Resources:

1.​ Vlab.amrita.edu Bioinformatics Virtual Lab I. II and III


2.​ https://youtube.com/playlist?list=PLTh2e5IZXW97zKZqqcfBNpQT1Y_zOdBO
H

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