Labmanual CS 1

BIOINFORMATICS
For Beginners
LABORATORY MANUAL
Prepared Under
DBT STAR COLLEGE SCHEME
Department of Computer Science
PSGR KRISHNAMMAL COLLEGE FOR WOMEN
College of Excellence
An Autonomous Institution - Affiliated to Bharathiar University
Reaccredited with ‘A’ Grade by NAAC
An ISO 9001:2015 Certified Institution
Peelamedu, Coimbatore – 641 004
Published by
BLUE HILL PUBLISHERS

Coimbatore - 641 113, Tamil Nadu, India.
Web: www.bluehillpublishers.com
Project 3_Lab Manual.indd 1 17/01/2019 4:34:55 PM

Title : Bioinformatics for Beginners Laboratory Manual
Language : English
Year : 2018
Author : Department of Computer Science
PSGR Krishnammal College for Women,
Coimbatore – 641 004, Tamil Nadu, India.
ISBN Number : 9788193708828
Copyright Warning : N
o part of this book may be reproduced or transmitted in any form or by
any means electronic or mechanical including photocopying or recording
or by any information storage and retrieval system without permission in
writing from PSGR Krishnammal College for Women, Coimbatore, Tamil
Nadu, India.
Published By : Blue Hill Publishers, Coimbatore.

EDITORS
Dr.M.S.Vijaya Dr.J.Viji Gripsy

Dr.S.C.Punitha Mrs.N.Deepa
Dr.S.Karpagavalli Mrs.J.Shalini
Dr.C.Arunpriya Mrs.N.A.Sheela Selvakumari
Mrs.R.Kavitha Dr.R.Vishnupriya
Mrs.A.S.Kavitha

PREFACE
Bioinformatics is the application of computational techniques and tools to

analyzeand manage biological data. The purpose of this laboratory manual is to pre-
sent a collection of laboratory techniques for the benefit of beginners in bioinfor-
matics. The emergence of bioinformatics is one of the biggest change happened to
biosciences in the last two decades.
The availability of gene, protein and genome sequences increased exponentially
in online data banks. To make sense of the innumerablebiological data, tools have
been developed to analyze the data efficiently to resolve various issues of science
and its application. This manual is been written specifically for the undergraduate,
non-science major students and introduces main biological databanks, their appli-
cations, and programs that helps to understand how to retrieve information from
the databases, and analyse the information to obtain useful knowledge about a DNA
sequence and its protein product.
This lab manual presents a collection of fourteen practical exercises, aimed
to provide standard protocols to access genome databank, perform sequence ali-
gnments, predicting primary, secondary and tertiary structure, visualization of
protein and construction of phylogenetic trees.This manual introduces the theory
and provides a systematic procedure to facilitate students to carry out the practical
exercises in an easy manner.Overall understanding of NCBI resources, accessing of
biological sequences from databank, performing sequence alignments and usage of
protein visualization tools will become easy if the students and researchers use this
manual effectively.
We also assure that this become a handy tool and motivation factor for the
basic researchers of bioinformatics.When the readers finish practising the exercises
in this manual they will be possessing knowledge to use the various on-line tools
available for processing the biological data and will provide a platform to develop
their skills in handling advanced bioinformatics techniques

CONTENT
S.No. Title Page No.
01 Exploration of the resources available in NCBI and PUBMED 1
02 Retrieval of a Genbank Entry using an accession number 5
03 Retrieval and analysis of a gene sequence “AF375082” in FASTA 9

format
04 Finding the official Symbol, alias name, chromosome number 13

and ID for gene using NCBI
05 Retrieval and analysis of a protein sequence from protein 17

database
06 Primary structure analysis of a protein 19
07 Secondary structure analysis of a protein 25
08 Tertiary protein structure analysis using RASMOL 27
09 Pair-wise and multiple sequence alignment using ClustalW 29
10 Pair-wise and multiple sequence alignment using BLAST 31
11 Alignment of two Sequences and determination of PAM Scoring 35

Matrix
12 Alignment of two Sequences and determination of BLOSUM 37

Scoring Matrix
13 Similarity Search using BLAST and Interpretation of Results 39
14 Conversion of Gene Sequence into its Corresponding Amino 41

Acid Sequence

BIOINFORMATICS FOR BEGINNERS
1. EXPLORATION OF THE RESOURCES AVAILABLE

IN NCBI AND PUBMED
Aim:
To explore the site map of NCBI and PUBMED and to study the resources avai-
lable on NCBI and PUBMED.
NCBI
The NCBI has developed many useful resources and tools, several of which
are described throughout this book. Of particular relevance to genome mapping is
the Genomes Division of Entrez. Entrez provides integrated access to different types
of data for over 600 organisms, including nucleotide sequences, protein sequences
with structures, PubMed, MEDLINE and genomic mapping information. The NCBI
Human Genome Map Viewer is a new tool that presents a graphical view of the
available human genome sequence data as well as cytogenetic, genetic, physical,
and radiation hybrid maps. The Map Viewer provides human genome sequence for
finished contigs, BAC tiling path of finished and draft sequence, location of genes,
STSs, and SNPs on finished and draft sequences; it is a useful tool for integrating
maps and sequence.
There are many other tools and databases at NCBI that are useful for gene
mapping projects including BLAST, GeneMap’99, LocusLink, OMIM , dbSTS, dbSNP,
dbEST, and UniGene databases. The BLAST can be used to search DNA sequen-
ces for the presence of markers, to confirm and refine map localizations. LocusLink
(Pruitt et al., 2000) presents information on official nomenclature, aliases, sequence
accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology,
map locations, and related Web sites. The dbSTS and dbEST databases themselves
play a lesser role in human and mouse gene mapping endeavors as their relevant
information has already been captured by other more detailed resources (LocusLink,
GeneMap’99, UniGene, MGD, and eGenome) but are currently the primary source of
genomic information for other organisms.
Department of Computer Science 1

Fig.1. Overview of the relationships in the Entrez integrated

information retrieval system.
Fig.2. Home page of NCBI
PUBMED:
PubMed contains all of MEDLINE, as well as citations provided directly by the
publishers. As such, PubMed contains more recent articles than MEDLINE, as well
as articles that may never appear in MEDLINE because of their subject matter. This
development led NCBI to introduce a new article identifier, called PubMed identifier
(PMID). Articles appearing in MEDLINE will have both a PMID and an MUID. Articles
appearing only in PubMed will have only a PMID.
2 Department of Computer Science

Fig.3. Home page of PubMed

PMID serves the same purpose as MUID in providing simple, reliable link to
the citation, means of linking records together and means of setting up hyperlinks.
Publishers have also started to send information on ahead-of-print articles
to PubMed, so this information may now appear before the printed journal. A new
project, PubMed Central, is meant to allow electronic publication to occur in lieu of
or ahead of publication in a traditional, printed journal. PubMed Central records
contain the full text of the article, not just the abstract, and include all figures and
references.

Fig.4. Search output screen of PUBMED
Result :
The NCBI and PUBMED websites are explored and the resources are studied.

2. RETRIEVAL OF A GENBANK ENTRY USING

AN ACCESSION NUMBER
Aim:
To retrieve a nucleotide sequence of interest from Genbank entry with Specific
accession number.
GenBank
GenBank® is the NIH genetic sequence database, an annotated collection of all
publicly available DNA sequences. GenBank is part of the International Nucleotide
Sequence Database Collaboration, which comprises the DNA Data Bank of Japan
(DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI.
These three organizations exchange data on a daily basis.
A GenBank release occurs in every two months and is available from the FTP
site. The release notes for the current version of GenBank provide detailed informa-
tion about the release and notifications of upcoming changes to GenBank. Release
notes for previous GenBank releases are also available. GenBank growth statistics
for both the traditional GenBank divisions and the WGS division are available from
each release.
An annotated sample GenBank record for a Saccharomyces cerevisiae gene
demonstrates many of the features of the GenBank flat file format.
Access to GenBank
There are several ways to search and retrieve data from GenBank.
 Search GenBank for sequence identifiers and annotations with Entrez Nucleo-
tide, which is divided into three divisions: CoreNucleotide (the main collection),
dbEST (Expressed Sequence Tags), and dbGSS (Genome Survey Sequences).
 Search and align GenBank sequences to a query sequence using BLAST (Basic
Local Alignment Search Tool). BLAST searches CoreNucleotide, dbEST, and
dbGSS independently.
 Search, link, and download sequences programmatically using NCBI e-utilities.
 The ASN.1 and flat file formats are available at NCBI’s anonymous FTP ser-
ver: ftp://ftp.ncbi.nlm.nih.gov/ncbi-asn1 and ftp://ftp.ncbi. nlm.nih.gov/
genbank.
GenBank Data Usage

The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA sequence
information. Therefore, NCBI places no restrictions on the use or distribution of the
GenBank data. However, some submitters may claim patent, copyright, or other

intellectual property rights in all or a portion of the data they have submitted. NCBI
is not in a position to assess the validity of such claims and therefore cannot provide
comment or unrestricted permission concerning the use, copying or distribution of
the information contained in GenBank.
Procedure:
1. Open the web browser and type the database address http://www.ncbi.nlm.
nih.gov/genbank/ in the address bar.
2. Type the query (i.e., the strain name for which the nucleotide sequence has to
be retrieved) in the search bar.
3. Select the particular sequence which is required.
4. Select FASTA format in the display settings and click apply.
5. Copy the sequence data and paste it in the notepad.
6. Save the notepad file in FASTA format.
7. Report the result.
Observations:
Fig.5. Home page of Genbank Data base

Fig.6. Search Output from Gen bank database of NCBI
Fig.7. Retrieved Nucleotide Sequence in FASTA Format
Result:
Thus the nucleotide sequence (Accession Number: E01306.1) was retrieved
from GenBank Database.

3. RETRIEVAL AND ANALYSIS OF A GENE SEQUENCE

“AF375082” IN FASTA FORMAT
Aim:
To retrieve the nucleotide sequence of interest from the National Center for
Biotechnology Information (NCBI) database.
NCBI Database:
The National Center for Biotechnology Information (NCBI) advances science
and health by providing access to biomedical and genomic information. NCBI crea-
tes public databases, conducts research in computational biology, develops software
tools for analyzing genome data, disseminates biomedical information for the better
understanding of diseases and molecular processes affecting human health. This
database groups biomedical literature, small molecules, and sequence data in terms
of biological relationships. It helps in retrieving DNA & peptide sequences, abstracts
to scientific articles, and structural coordinates to visualize the 3D structure of resol-
ved molecules.
Procedure:
1. Open the web browser and type the database address www.ncbi.nlm.nih.gov
in the address bar.
2. Type the query, AF375082 (i.e., the accession number of a gene for which the
nucleotide sequence has to be retrieved) in the search bar.
5. Copy the sequence data and paste it in the notepad.
6. Save the notepad file in FASTA format.

Observations:
Fig.8. List of information available in NCBI Database
Fig.9. Details of hemagglutinin coding sequence retrieved from NCBI

Fig.10. Hemagglutinin coding sequence (AF375082) in FASTA format
Result:
Thus the nucleotide sequence of AF375082 was retrieved from NCBI Database.

4. FINDING THE OFFICIAL SYMBOL, ALIAS NAME,

CHROMOSOME NUMBER AND ID
FOR GENE USING NCBI
Aim:
To analyze the NCBI web site and find the official gene symbol, its alias name,
chromosome number and its ID.
Procedure:
1. Open the web browser and type the database address http://www.ncbi.nlm.
nih.gov/gene/ in the address bar.
2. Type the query (i.e., the strain name for which the nucleotide sequence has to
be retrieved) in the search bar.
3. Select the particular sequence which requires the official gene symbol, name,
chromosome number and its ID.
5. Down load the file in FASTA format.
Fig.11. Home page of the Data Bank “Gene”

Fig.12. Search output from the “Gene” data bank
Fig.13. Entries about a gene (BDNF – Brain Derived Neurotrophic Factor) available
in “Gene” data bank

Output:
Kingdom: Eukaryota
Subgroup: Mammals
Sequence data: genome assemblies: 43
Haploid chromosomes: 48
Result:
The official gene symbol, alias name, chromosome number and ID has been
retrieved from the NCBI.

5. RETRIEVAL AND ANALYSIS OF PROTEIN SEQUENCE

FROM PROTEIN DATABASE
Aim:
To analyse and retrieve the protein sequence of a protein from the Protein Data
Bank (PDB) database.
Protein Data Bank:

PDB is a worldwide repository for the 3D structure of the macromolecules such
as proteins and nucleic acids. The database is operated by the Research Collabo-
rator for Structural Bioinformatics (RCSB). This database contains the X-ray and
NMR structures of the proteins, nucleic acids and protein-nucleic acid complexes.
Along with the structures PDB aids in providing other associated information like
the sequence details, atomic coordinates, crystallization conditions, structural nei-
ghbours and links to other databases. Every entry entered in this database has a
unique identification, which is a four-letter word. The ID starts with a number fol-
lowed by three letters or two letters and a number, the alphabets are in upper case.
Procedure:
1. Open the web browser and type the database address www.pdb.org in the
address bar.
2. Type the query (i.e., the protein name for which the amino acid sequence has
to be retrieved) in the search bar of the home page.
4. Download the file in FASTA format from the option “Download Files”.

Observation:
Fig.14. Information on an antimicrobial protein in PDB Database
The retrieved sequence is

>2L24:A|PDBID|CHAIN| SEQUENCEIFGAIAGFIKNIWX
Organism : Influenza A virus.
Protein : Hemagglutinin
Accession No : 2L24
Length : 14aa
Result:
Thus the required protein sequence is retrieved from the PDB database.

6. PRIMARY STRUCTURE ANALYSIS OF A PROTEIN

(i) Retrieval of Primary Protein Structure
Aim:
To retrieve the structure of a protein from Protein Data Bank (PDB) database.
Protein Data Bank:

Proteins are made up of polypeptide chains, which are amino acids joined toge-
ther with peptide bonds. The unique sequence of amino acids that make up a protein
or polypeptide chain is called the Primary Structure.
Fig.15. Primary structure of protein

The sequence of a protein is determined by the DNA of the gene that enco-
des the protein. A change in the gene’s DNA sequence may lead to a change in the
amino acid sequence of the protein. Even changing just one amino acid in a protein’s
sequence can affect the protein’s overall structure and function.
Procedure:
address bar.
2. Type the query (the protein name for which structure has to be retrieved) in
the search bar of the home page.
3. Select the protein of interest.
4. Download the file in PDB format from the option “Download Files”.

Observation:
Fig.16. Information of desired protein from PDB Database
Organism : Bacillus subtilis

Protein : Stage III sporulation protein D
Accession ID : 2L0K:A
Method used : NMR
>2LOK:A|PDBID|CHAIN|SEQUENCEMSPIPLPVTDTDDAWRARIAAHRADKDEFLAT
HDQSPIPPADRGAFDGLRYFDIDASFRVAARYQPARDPEAVELETTRGPPAEYTRAAVLG
FDLGDSHHTLTAFRVEGESSLFVPFTDETTDDGRTYEHGRYLDVDPAGADGGDEVAL-
DFNLAYNPFCAYGGSFSCALPPADNHVPAAITAGERVDADLEHHHHHH
Result:
The required primary protein structure is retrieved from the Protein Database
in PDB format.

(ii). Analysis of primary protein structure
Aim:
To compute the physical and chemical parameters of the given protein.
ProtParam:
ProtParam (Protein Parameters) is a tool which allows the computation of
various physical and chemical parameters for a given protein stored in Swiss-Prot or
TrEMBL or for a user entered sequence. The computed parameters include the mole-
cular weight, theoretical pI, amino acid composition, atomic composition, extinction
coefficient, estimated half-life, instability index, aliphatic index and grand average of
hydropathicity.
Procedure:
1. Open the web browser and type the database address www.expasy.org/tools
in the address bar.
2. Select ProtParam from the list of displayed tools.
3. Paste the query sequence in the box given.
4. Click the option “Compute Parameters”.
Observations:
Fig.17. ProtParam Home page

Fig.18. Amino acid content and other basic information of a given protein in
ProtParam
Fig.19. Atomic content and few other physio-chemical features of a given protein in
ProtParam

The computed parameters are,
Number of amino acids 380
Molecular Weight 42443.0
Theoretical pI 8.38
Total number of negatively charged 15

residues (Asp + Glu)
Total number of positively charged 17

residues (Arg + Lys)
Total number of atoms 6052
Extinction Coefficient 85495
Result:
Thus, protein parameters were computed using ProtParam tool.

7. SECONDARY STRUCTURE ANALYSIS OF A PROTEIN
Aim:
To retrieve the secondary structure of a protein from Protein Data Bank (PDB)
database.
Protein Data Bank:

Secondary structures are ordered structures formed by internal hydro-
gen bonding between amino acid residues. The common secondary structures are
α-helix, β-strand, loops and turns. More information is given below about secondary
structures.
The secondary structure of protein refers to local folded structures that
form within a polypeptide due to interactions between atoms of the backbone. The
backbone just refers to the polypeptide chain apart from the R groups. Both α-helix
and β-strand are held in shape by hydrogen bonds that form between the carbonyl O
of one amino acid and the amino H of another.
Fig.20. Secondary structures of Protein
Procedure:
address bar.
2. Type the query (i.e., the protein name for which structure has to be retrieved)
in the search bar of the home page.
3. Select the protein of interest.
4. Click on the required part of the protein

Observation:
Fig.21. Information of desired protein from PDB Database

Protein : Stage III sporulation protein D
Accession ID : 2L0K:A
Result:
The required secondary protein structure is retrieved from the Protein Data-
base in pdb format.

8. TERTIARY PROTEIN STRUCTURE ANALYSIS USING

RASMOL
Aim:
To view the tertiary structure and analyze the protein using Rasmol.
RasMol:
RasMol is a computer program written for molecular graphics visualization
intended and used primarily for the depiction and exploration of biological macro-
molecule structures, such as those found in the Protein Data Bank. It was originally
developed by Roger Sayle in the early 90s.
Procedure:
1. Open the working page of offline tool.
2. Upload the pdb file of desired protein.
3. Structure will be displayed.
4. View the different forms of structure using display option.
5. Change the format into GIF in export option.
Observation:
Fig.22. 3D Structure of a protein visualized using “RasMol”
Result:
Thus, the tertiary structure of protein is viewed in Rasmol.

9. PAIR-WISE SEQUENCE ALIGNMENT AND MULTIPLE

SEQUENCE ALIGNMENT USING CLUSTALW
Aim:
To perform pair wise and multiple sequence alignment using clustalw for given
sequences.
Procedure:
1. Open the web browser and type www.ebi.ac.uk/Tools/msa/ clustalw.
2. Upload the sequences from the Notepad or paste the sequences in FASTA
format.
3. Upload two sequences for pair-wise alignment or more than two sequences for
multiple sequence alignment After uploading, choose the “Execute Multiple
Alignment” option in the alignment icon.
4. Sequence alignment results will be appeared within few seconds after
execution.
Observation:
Fig.23. Query window of CLUSTALW

Fig.24. Alignment of retrieved sequences using CLUSTALW tool.
Result:
Thus the given sequences are aligned using ClustalW.

10. PAIR WISE AND MULTIPLE SEQUENCE ALIGNMENT

USING BLAST
Aim:
To perform pair wise and multiple sequence alignment using BLAST tool.
Sequence Similarity:
Database Similarity Searches have become a mainstay of Bioinformatics.
Sequence database searches can also be remarkably useful for finding the function
of genes whose sequences have been determined in the laboratory. The sequence of
the gene of interest is compared to every sequence in a sequence database, and the
similar ones are identified. Alignments with the best-matching sequences are shown
and scored. If a query sequence can be readily aligned to a database sequence of
known function, structure, or biochemical activity, the query sequence is predicted
to have the same function, structure, or biochemical activity.
Pairwise sequence alignment methods are concerned with finding the best-
matching piecewise local or global alignments of protein (amino acid) or DNA (nucleic
acid) sequences. Multiple alignment is an extension of pairwise alignment to incor-
porate more than two sequences into an alignment. Multiple alignment methods try
to align all of the sequences in a specified set.
BLAST
BLAST is an acronym for Basic Local Alignment Search Tool. BLAST is a sophi-
sticated software package that has become the single most important piece of sof-
tware in the field of Bioinformatics. The following tools are different type of blast
programs used with respect to the aim of the user.
Blast programs:
 BLASTp – Compares an amino acid query sequence against a protein sequence
database.
 BLASTn – Compares a nucleotide query sequence against a nucleotide sequence
database.
 BLASTx – Compares a nucleotide query sequence translated in all reading fra-
mes against a protein sequence database.
 tBLASTn – Compares a protein query sequence against a nucleotide sequence
database dynamically translated in all reading frames.
 tBLASTx – Compares the six frame translation of a nucleotide query sequence
against the 6 frame translation of a nucleotide sequence database.
 Megablast – For highly similar sequences.

Modes of BLAST:
1. PHI BLAST
2. PSI BLAST
1. PHI BLAST
Pattern Hit Intiated BLAST (PHI-BLAST) searches protein sequences using a combi-
nation of pattern matching and local alignment to reduce the probability of false posi-
tives. This option matches a regular expression that is specified. Given a sequence
and a pattern that is occurring within that sequence this program finds all the other
sequences that is occurring in that sequence.
2. PSI BLAST
Position Specific Initiated BLAST (PSI-BLAST) refers to a feature of BLAST 2.0 in
which a profile automatically froms a multiple alignment of the highest scoring hits
in an initial BLAST search. The PSSM is generated by calculating position-specific
scores for each position in the alignment. Highly conserved positions receive high
scores and weakly conserved positions receive scores near zero.
Fig.25. Home page of BLAST

Procedure:
1. Open the web browser and type http://blast.ncbi.nlm.nih.gov/ Blast.cgi
2. Click either nucleotide blast or protein blast icon according to the requirement
3. Select “Align two or more sequences” check box for opting multiple sequence
alignment or deselect for pair wise alignment
4. Upload or paste a query sequence (in FASTA format) in the query box and
execute BLAST for pair wise alignment. This will be identifying most similar
sequences from the databank.
5. Upload or paste a query sequence (in FASTA format) in the query box and
upload more than one sequences (in FASTA format) in the subject box and
then execute BLAST for multiple sequence alignment. This will be identifying
the similarity /dissimilarity among the sequences.
Observation :
Fig. 26. Pair-wise sequence alignment using BLAST identified similar sequences
from databanks

Fig. 27. Multiple sequence alignment using BLAST identified similarity between
query sequence and other sequences
Result:
Thus the given sequences are aligned using BLAST

11. ALIGNMENT OF TWO SEQUENCES AND

DETERMINATION OF
PAM SCORING MATRIX
Aim:
To align two different sequences using Fold and Function Assignment System
(FFAS).
Procedure:
1. Open the web browser and type www.ffas.ycrf.edu in the address bar.
2. Open the “Pair-wise Alignment” link in the home page of FFAS.
3. Paste the queries in FASTA format in two different dialogue boxes.
Observation:
Fig.28. Alignment of two retrieved sequences using FFAS tool

Fig.29. Alignment of two retrieved sequences using PAM matrix in FFAS tool
Sequences aligned:
Database ID Source Organism Length
2Y71:A 3-Dehydroquinate dehydratase Escherichia coli 146
2Y76:A 3-Dehydroquinate dehydratase Escherichia coli 146
% Identity : 100%
% Gap : 0%
Expected Value : -0.952E+02
Result:
Thus the two sequences are aligned pair-wise using Fold and Function Assi-
gnment System.

12. ALIGNMENT OF TWO SEQUENCES AND

DETERMINATION OF BLOSUM SCORING MATRIX
Aim:
To align two sequences and find the BLOSUM scoring matrix.
Procedure:
1. Open the browser and type www.ebi.ac.uk/Tools/msa/clustalw2.
2. Upload the sequences from the Notepad or paste the sequences in FASTA
format.
3. Choose the “Full Alignment” option in the alignment icon.
4. Choose BLOSUM Matrix from the matrix option.
5. Multiple sequence alignment is shown.
Observation:
Fig.30. Alignment of retrieved sequences using CLUSTALW tool.
Result:
Thus the given three sequences are aligned using ClustalW with BLOSUM
Marix.

13. SIMILARITY SEARCH USING BLAST AND

INTERPRETATION OF RESULTS
Aim:
To search the similar sequence of given query using Basic Local Alignment
Search Tool (BLAST).
BLAST:
The BLAST finds regions of local similarity between sequences. The program com-
pares nucleotide or protein sequences to sequence databases and calculates the stati-
stical significance of matches. BLAST can be used to infer functional and evolutionary
relationships between sequences and helps to identify the members of gene families.
Procedure:
1. Open the web browser and type the database address www.ncbi.nlm.nih.gov/
blast/ in the address bar.
2. Upload or paste the sequence, for which the similar sequences have to be
retrieved, in the dialogue box, in FASTA format.
3. Click “Begin Search” option so that the page containing the organism’s ID and
other details are displayed.
4. Click “View Reports” and the sequences similar to the given sequence of inte-
rest are displayed.
5. Report the sequences which have maximum identity and similarity.
Observation:

Fig.31. Similarity search output map for a nucleotide sequence in BLAST
Fig.32. Information regarding the similarity searches for a nucleotide sequence
Query ID : lcl|3351
Nucleotide : 16S ribosomal RNA
Query length : 300 bp
Retrieved similar sequences
ID NO. E-value %identity %gap Length of the sequence
NT 011520.12 2.6 100 0 21
NW001838745.1 2.6 100 0 21
Result:
The similar sequences were retrieved and the % gap, %identity and the expected
value for the sequences were known.

14. CONVERSION OF GENE SEQUENCE INTO ITS

CORRESPONDING AMINO ACID SEQUENCE
Aim:
To convert the given gene sequence into its corresponding amino acid sequence.
Procedure:
1. Open the web browser and type the database address www.expasy.org/tools
in the address bar.
2. Select TRANSLATE from the list of displayed tools.
3. Paste the query sequence in the given box.
4. Click TRANSLATE option.
Observation:
Fig.33. Home Page of Translate Tool

Fig.34. Translated Amino Acid Sequence
Organism : Escherichia coli

Accession number : JF321293
Result:
Thus the given gene sequence is converted into its corresponding Protein
sequence.

EXPERT REVIEW
The manual on Bioinformatics – For Beginners, would

be highly useful for all the beginners of Bioinformatics
from the academia or research. The experiments desi-
gned are highly appropriate to get familiar with most
important biological databases like NCBI and biomole-
cule analysis tools such as BLAST, ClustalW, RasMol.
The data retrieval and analysis using these experi-
ments could give a logical understanding to the begin-
Dr. T. Balasaravanan ners. I appreciate the effort of the editors for the way
Assistant Professor
of introducing the experiments with a clear theoretical
Department of Botany
base which made the manual most useful. I wish them
Government Arts College
Udumalpet - 642 126 to come out with more useful outcomes to the society.
The laboratory manual “Bioinformatics- For Beginners

“has covered the basic themes required for understan-
ding DNA and Protein sequence analysis in a well defi-
ned manner.
Merits
1. This book is very helpful for beginners as they can gain
knowledge in basic tools and databases of bio informa-
tics like BLAST, RASMOL, ClustalW, NCBI etc.
2. Students can gain knowledge in Pair-wise sequence
Dr S.Meenatchi Sundaram
and Multiple Sequence by the above mentioned tools.
Associate Professor &
3. The content was neatly planned and well organized,
Director (Research),
which helps the student to know the basics of bioin-
Department of Microbiology,
formatics and enrich their knowledge in Structure
Nehru Arts and Science,
Analysis of Protein and Sequence alignment using
Coimbatore -641 105
Bioinformatics tools.
The following suggestions can improve the manual further

1. The titles of experiment can be changed into thematic topics Eg: Retrieve –
Retrieval; Convert – Conversion; Getting- Retrieval
2. Figure Numbers can be given to each figure (Eg:Fig.1, Fig.2 etc)


Labmanual CS 1

Uploaded by

Copyright:

Available Formats

Labmanual CS 1

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Labmanual CS 1

Uploaded by

Copyright:

Available Formats

BIOINFORMATICS

BLUE HILL PUBLISHERS

Project 3_Lab Manual.indd 1 17/01/2019 4:34:55 PM

Author : Department of Computer Science

PSGR Krishnammal College for Women,

Coimbatore – 641 004, Tamil Nadu, India.

ISBN Number : 9788193708828

Published By : Blue Hill Publishers, Coimbatore.

Project 3_Lab Manual.indd 2 17/01/2019 4:34:55 PM

Dr.M.S.Vijaya Dr.J.Viji Gripsy

Project 3_Lab Manual.indd 3 17/01/2019 4:34:55 PM

Bioinformatics is the application of computational techniques and tools to

Project 3_Lab Manual.indd 5 17/01/2019 4:34:55 PM

S.No. Title Page No.

01 Exploration of the resources available in NCBI and PUBMED 1

02 Retrieval of a Genbank Entry using an accession number 5

03 Retrieval and analysis of a gene sequence “AF375082” in FASTA 9

04 Finding the official Symbol, alias name, chromosome number 13

05 Retrieval and analysis of a protein sequence from protein 17

06 Primary structure analysis of a protein 19

07 Secondary structure analysis of a protein 25

08 Tertiary protein structure analysis using RASMOL 27

09 Pair-wise and multiple sequence alignment using ClustalW 29

10 Pair-wise and multiple sequence alignment using BLAST 31

11 Alignment of two Sequences and determination of PAM Scoring 35

12 Alignment of two Sequences and determination of BLOSUM 37

13 Similarity Search using BLAST and Interpretation of Results 39

14 Conversion of Gene Sequence into its Corresponding Amino 41

Project 3_Lab Manual.indd 7 17/01/2019 4:34:56 PM

1. EXPLORATION OF THE RESOURCES AVAILABLE

Department of Computer Science 1

Project 3_Lab Manual.indd 1 17/01/2019 4:34:56 PM

Fig.1. Overview of the relationships in the Entrez integrated

Fig.2. Home page of NCBI

2 Department of Computer Science

Project 3_Lab Manual.indd 2 17/01/2019 4:34:56 PM

Fig.3. Home page of PubMed

Department of Computer Science 3

Project 3_Lab Manual.indd 3 17/01/2019 4:34:56 PM

Fig.4. Search output screen of PUBMED

4 Department of Computer Science

Project 3_Lab Manual.indd 4 17/01/2019 4:34:56 PM

2. RETRIEVAL OF A GENBANK ENTRY USING

GenBank Data Usage

Department of Computer Science 5

Project 3_Lab Manual.indd 5 17/01/2019 4:34:56 PM

Fig.5. Home page of Genbank Data base

6 Department of Computer Science

Project 3_Lab Manual.indd 6 17/01/2019 4:34:56 PM

Fig.6. Search Output from Gen bank database of NCBI

Fig.7. Retrieved Nucleotide Sequence in FASTA Format

Department of Computer Science 7

Project 3_Lab Manual.indd 7 17/01/2019 4:34:56 PM

3. RETRIEVAL AND ANALYSIS OF A GENE SEQUENCE

Department of Computer Science 9

Project 3_Lab Manual.indd 9 17/01/2019 4:34:56 PM

Fig.8. List of information available in NCBI Database

Fig.9. Details of hemagglutinin coding sequence retrieved from NCBI

10 Department of Computer Science