LABORATORY MANUAL
BTY320
BIOINFORMATICS LABORATORY
(For private circulation only)
Name of the Student………………………………………………...
Registration Number/Roll No………………………………………
Section and Group…………………………………………………...
School of Biotechnology and Biosciences
Session Term:
LMBTY320 Page 1
General Guidelines for the students:
First practical session and first practical session after MTE are for introduction to all the
experiments before and after MTE respectively.
Students are expected to follow the instructions attentively and, before coming to the
subsequent labs they should browse through the database and tools.
Student should attend theory class so that they can clearly understand the theory behind the
experiments. They should keenly observe and understand the database structure which are
demonstrated in class.
Compulsory things to be carried by the students in lab: Lab manual.
Do’s:
1. Do write all the points discussed in lab.
2. Lab manual should contain all experiments, complete lab manual along with front page,
table of content should be brought.
3. Keep your cell phone in bags in switched off/silent mode.
4. Always be punctual in lab otherwise no attendance will be awarded.
Don’ts:
1. Don’t Share lab manuals/ worksheets.
2. Don’t talk among yourselves.
3. Don’t copy the result.
4. Don’t roam around in lab.
5. Don’t open restricted sites in lab.
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Table of Contents
S. No. Page No.
Title of Experiment
1 Sequence database- GenBank 4–7
2 Sequence database UniProtKB- Swissprot 8 – 11
3 Sequence Alignment Tools: DOTTUP 12 – 16
4 Sequence Alignment Tools: NEDDLE & WATER 17 – 21
5 Sequence Alignment Tools: ClustalW 22 – 26
Sequence Based Database Search and Gene prediction : Gene
6 Prediction Method 27 - 31
7 Sequence Based Database Search and Gene prediction : BLAST 32 – 36
8 Protein Structure Prediction Tool/Software : GOR 37 - 41
9 Protein Structure Prediction Tool/Software : JPRED 42 - 46
10 Protein Structure Prediction Tool/Software : Swiss Model 47 - 51
Reference Book:
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Baxevanis
and Ouellette. Wiley InterScience, Second Edition.
Other Readings:
Bioinformatics: Sequence and Genome Analysis, David W. Mount, Cold Spring
Harbor Laboratory Press Fifth Edition, (2005).
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Experiment 1
1. Experiment: Sequence database- GenBank
Equipment Required: Computer with internet connection.
2. Learning Objectives:
The student will know the importance of biological database.
The student will learn to classify database on the basis of the information stored.
The students will also learn to select database to be used on the basis of problem stated.
3. Theory/Principle/Background of the topic: 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
Databank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and
GenBank at NCBI. These three organizations exchange data on a daily basis. This database
is produced and maintained by the National Center for Biotechnology Information (NCBI)
as part of the International Nucleotide Sequence Database Collaboration (INSDC). The
National Center for Biotechnology Information is a part of the National Institutes of Health
in the United States. GenBank and its collaborators receive sequences produced in
laboratories throughout the world from more than 100,000 distinct organisms. In the more
than 30 years since its establishment, GenBank has become the most important and most
influential database for research in almost all biological fields, whose data are accessed and
cited by millions of researchers around the world. GenBank continues to grow at an
exponential rate, doubling every 18 months.
4. Outline of Procedure:
1. Visit the homepage of NCBI and scroll through the list of multiple databases
maintained by NCBI.
2. Change the all database option to the nucleotide option.
3. Specify the text query in search box (e.g. insulin).
4. Go to the “Advanced” option, select field name as protein name and then type insulin
for search. Note the results are refined.
5. Add more fields, use Boolean operators and go for advanced search (e.g. Protein name
– insulin AND Organism - human).
6. Explore the limits option to specify date of submission, source database etc. Open one
record after refinement and note the major annotations.
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5. General calculations: Difference in number of records after each refinement. (Q1-Q2) hits.
6. Results:
1. Number of records obtained after performing search.
2. Number of records obtained after search refinement.
7. Scope of result: Students will know annotations of relevant record like molecule type,
source, length, functions and features including sequence details.
8. Results required: Parameter: Limits, advanced.
9. Cautions: Refined search to be performed.
Suggested Reading:
Websites:
http://www.ncbi.nlm.nih.gov/
http://www.ncbi.nlm.nih.gov/genbank/samplerecord/
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Date of Performance Worksheet of the student Registration Number:
Aim:
Observations:
Calculations:
Result and Discussion:
LMBTY320 Page 6
Learning Outcome
To be filled in by Faculty
S. No. Parameter Marks Max. Marks
obtained
1 Understanding of the student about the 20
procedure/apparatus.
2 Observations and analysis including learning 20
outcomes.
3 Completion of experiment, Discipline and 10
Cleanliness.
4 Signature of Faculty.
LMBTY320 Page 7
Experiment 2
1. Experiment: Sequence database UniProtKB- Swissprot Introduction to
access Equipment Required: Computer with internet connection.
2. Learning Objectives:
The student will learn to search for protein of interest in a refined and least redundant form.
The students will also understand difference between protein and nucleotide annotations.
3. Theory/Principle/Background of the topic: Swiss-Prot (created in 1986) is a high quality
manually annotated and non-redundant protein sequence database, which brings together
experimental results, computed features and scientific conclusions. UniProtKB/Swiss-Prot is
now the reviewed section of the UniProt Knowledgebase.
The TrEMBL section of UniProtKB was introduced in 1996 in response to the increased
dataflow resulting from genome projects. It was already recognized at that time that the
traditional time- and labour-consuming manual annotation process which is the hallmark of
Swiss-Prot could not be broadened to encompass all available protein sequences. Publicly
available protein sequences obtained from the translation of annotated coding sequences in the
EMBL-Bank/GenBank/DDBJ nucleotide sequence database are automatically processed and
entered in UniProtKB/TrEMBL where they are computed-annotated in order to make them
swiftly available to the public. UniProtKB/TrEMBL contains computationally analysed
records that are enriched with automatic annotation and classification. These
UniProtKB/TrEMBL unreviewed entries are kept separated from the UniProtKB/Swiss-Prot
manually reviewed entries so that the high quality data of the latter is not diluted in any way.
4. Outline of Procedure:
1. Open the UniProt website. Under Databases choose UniProtKB.
2. Type the query “reviewed: yes” in search box.
3. On pressing search only SwissProt results will be displayed, add more query words like
reviewed: yes insulin.
4. Go for advanced search, select fields and then see refined results.
5. Add more fields like organism, gene name.
6. Open record obtained after refinement, note the major annotations.
5. General calculations: Difference in number of records after each refinement. (Q1-Q2)
6. Results:
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1. Number of records obtained after performing search.
2. Number of records obtained after search refinement.
7. Scope of result: Students will know annotations of relevant record like molecule type,
source, length, functions and features, gene ontology, subcellular location, PTM, secondary
structure, sequence details etc.
8. Results required: Parameter: Advanced.
9. Cautions: Refined search to be performed
Suggested Reading:
Websites:
http://www.uniprot.org/help/
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Date of Performance Worksheet of the student Registration Number:
Aim:
Observations:
Calculations:
Result and Discussion:
LMBTY320 Page 10
Learning Outcome
To be filled in by Faculty
S. No. Parameter Marks Max. Marks
obtained
1 Understanding of the student about the 20
procedure/apparatus.
2 Observations and analysis including learning 20
outcomes.
3 Completion of experiment, Discipline and 10
Cleanliness.
4 Signature of Faculty.
LMBTY320 Page 11
Experiment 3
1. Experiment: Sequence Alignment Tools: DOTTUP
Equipment Required: Computer with internet connection.
2. Learning Objectives: To acquaint students with the sequence comparison and
analysis tool.
3. Theory/Principle/Background of the topic: Dot plot is a graphical method that allows
the comparison of two biological sequences and identifies regions of close similarity
between them. For a simple visual representation of the similarity between two sequences,
individual cells in the matrix can be shaded black if residues are identical, so that matching
sequence segments appear as runs of diagonal lines across the matrix. Some idea of the
similarity of the two sequences can be gleaned from the number and length of matching
segments shown in the matrix. Identical proteins will obviously have a diagonal line in the
center of the matrix. Insertions and deletions between sequences give rise to disruptions in
this diagonal. Regions of local similarity or repetitive sequences give rise to further
diagonal matches in addition to the central diagonal. Because of the limited protein
alphabet, many matching sequence segments may simply have arisen by chance. One way
of reducing this noise is to only shade runs or 'tuples' of residues, e.g. a tuple of 3
corresponds to three residues in a row. This is effective because the probability of matching
three residues in a row by chance is much lower than single-residue matches. Dot plots are
one of the oldest ways of comparing two sequences
4. Outline of Procedure:
1. Explore the sequence alignment tools available at EMBOSS.
2. Select two sequence that are expected to share functional similarity or homology.
Perform pairwise alignment using the program Dottup.
3. Analyse the diagonals observed as output.
4. Identify indels, repeats etc.
5. Change the word size and repeat the steps, observe the difference and influence of
word size.
5. General calculations: Count the number of diagonals observed for different word size.
6. Results:
Diagonals obtained after alignment.
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7. Scope of result: Students will get information about repeats, indels and different parameters
to be used in this experiment.
8. Results required: Parameter: Word size.
9. Cautions: Significant word size to be used.
Suggested Reading:
Websites:
http://emboss.bioinformatics.nl/cgi-bin/emboss/help/dottup
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Date of Performance Worksheet of the student Registration Number:
Aim:
Observations:
Calculations:
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Result and Discussion:
Learning Outcome
LMBTY320 Page 15
To be filled in by Faculty
S. No. Parameter Marks Max. Marks
obtained
1 Understanding of the student about the 20
procedure/apparatus.
2 Observations and analysis including learning 20
outcomes.
3 Completion of experiment, Discipline and 10
Cleanliness.
4 Signature of Faculty.
LMBTY320 Page 16
Experiment 4
1. Experiment: Sequence Alignment Tools: NEDDLE & WATER.
Equipment Required: Computer with internet connection.
2. Learning Objectives: To acquaint students with the pairwise sequence alignment
tools.
To help students understand difference between global and local alignment tool.
3. Theory/Principle/Background of the topic: Closely related sequences which are of
same length are very much appropriate for global alignment. Here, the alignment is carried
out from beginning till end of the sequence to find out the best possible alignment. The
Needleman–Wunsch algorithm is an algorithm used in bioinformatics to align protein or
nucleotide sequences. It was published in 1970 by Saul B. Needleman and Christian D.
Wunsch it uses dynamic programming, and was the first application of dynamic
programming to biological sequence comparison. It is sometimes referred to as the optimal
matching algorithm. The Smith–Waterman algorithm performs local sequence alignment;
that is, for determining similar regions between two strings or nucleotide or protein
sequences. Instead of looking at the total sequence, the Smith– Waterman algorithm
compares segments of all possible lengths and optimizes the similarity measure.
4. Outline of Procedure:
1. Explore the sequence alignment tools available at EMBOSS.
2. Select two sequences that are expected to share high functional similarity or
homology. Perform pairwise alignment using the program Needle.
3. Select two sequences that are expected to share distant functional similarity or
homology and have significantly different length. Perform pairwise alignment using the
program Water.
4. Analyze the output (alignment score, identity, similarity, gaps etc.)
5. General calculations: Alignment score. Number of matches*match score + number of
mismatches* mismatch score + number of gaps*gap penalty(opening/extension).
6. Results: Global and local alignment of input sequences.
7. Scope of result: Students will get information about sequence identity, similarity and its
importance to establish homology.
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8. Results required: Parameter: Gap penalty.
9. Cautions: Suitable scoring matrix to be used.
Suggested Reading:
Websites:
http://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-
biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture3.pdf
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Date of Performance Worksheet of the student Registration Number:
Aim:
Observations:
Calculations:
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Result and Discussion:
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Learning Outcome
To be filled in by Faculty
S. No. Parameter Marks Max. Marks
obtained
1 Understanding of the student about the 20
procedure/apparatus.
2 Observations and analysis including learning 20
outcomes.
3 Completion of experiment, Discipline and 10
Cleanliness.
4 Signature of Faculty.
LMBTY320 Page 21
Experiment 5
1. Experiment: Sequence Alignment Tools: ClustalW.
Equipment Required: Computer with internet connection.
2. Learning Objectives: To acquaint students with multiple sequence alignment tools.
Students will also learn to identify conserved regions and perform phylogenetic analysis.
3. Theory/Principle/Background of the topic: Multiple Sequence Alignment (MSA)
refers to sequence alignment of three or more biological sequences, generally protein, DNA, or
RNA. In many cases, the input set of query sequences are assumed to have an evolutionary
relationship by which they share a lineage and are descended from a common ancestor. From
the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be
conducted to assess the sequences' shared evolutionary origins. ClustalW2 (newer version of
ClustalW) is a general purpose multiple sequence alignment program for DNA or proteins.
There are three main steps: do pairwise alignment of every possible pair, create a guide tree,
and use the guide tree to carry out a multiple alignment. Distance among the sequences are
calculated by adding the horizontal branches of tree.
4. Outline of Procedure:
1. Visit the website of online MSA tool ClustalW.
2. Explore the different input options (e.g., tree, scoring scheme etc.).
3. Enter the query sequences in multi fasta format.
4. Perform MSA.
5. Analyse the output (colour option, phylogenetic tree, similar, Identical, * etc.).
6. Observe how the tree display changes between cladogram and real.
5. General calculations: Distance between all sequence pair. Add all the horizontal distance.
6. Results: Phylogenetic tree, conserved residue.
7. Scope of result: The scope of this experiment is to get evolutionary relations
among different species/organisms.
8. Results required: Parameter: Scoring matrix.
9. Cautions: Multi FASTA format to be used as input.
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Suggested Reading:
Websites:
http://www.ebi.ac.uk/Tools/msa/clustalw2/help/faq.html
LMBTY320 Page 23
Date of Performance Worksheet of the student Registration Number:
Aim:
Observations:
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Calculations:
Result and Discussion:
LMBTY320 Page 25
Learning Outcome
To be filled in by Faculty
S. No. Parameter Marks Max. Marks
obtained
1 Understanding of the student about the 20
procedure/apparatus.
2 Observations and analysis including learning 20
outcomes.
3 Completion of experiment, Discipline and 10
Cleanliness.
4 Signature of Faculty.
LMBTY320 Page 26
Experiment 6
1. Experiment: Sequence Based Database Search and Gene prediction: Gene Prediction
Method Equipment Required: Computer with internet connection.
2. Learning Objectives: To acquaint students with genome sequence analysis for
functional annotation and prediction of coded products.
3. Theory/Principle/Background of the topic: The ORF Finder (Open Reading Frame
Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum
size in a user's sequence or in a sequence already in the database. This tool identifies all open
reading frames using the standard or alternative genetic codes. The deduced amino acid sequence
can be saved in various formats and searched against the sequence database using the BLAST
server. The ORF Finder is helpful in preparing complete and accurate sequence submissions. It is
also packaged with the Sequin sequence submission software. Gene prediction is one of the key
steps in Genome annotation, following Sequence assembly, the filtering of non-coding regions
and repeat masking. Many aspects of structural gene prediction are based on current
understanding of underlying biochemical processes in the cell such as gene transcription,
translation, protein–protein interactions and regulation processes, which are subject of active
research in the various omics fields such as Transcriptomics, Proteomics, Metabolomics, and
more generally structural and functional genomics.
4. Procedure:
1. Select genomic sequence fragment for prediction of coding region.
2. Use default threshold value and genetic code. Perform gene prediction.
3. Explore the different input options (e.g., threshold value, genetic code etc.). Change these
parameters to check difference in results.
4. Analyse the output (reading frame, length, span of coding region etc.).
5. Compare the longest ORF product across protein database.
5. General calculations: Statistical significance of ORFs, calculate random expected
probability of finding termination codon, compare with observed probability.
6. Results:
Number of Open Reading Frames obtained after performing search.
7. Scope of result: This experiment will predict possible coding regions or genes. The
LMBTY320 Page 27
output will facilitate genome annotation.
8. Results required: Parameter: Threshold.
9. Cautions: Highest length ORF to be used for further comparison.
Suggested Reading:
Books:
NCBI Handbook.
LMBTY320 Page 28
Date of Performance Worksheet of the student Registration Number:
Aim:
Observations:
Calculations:
LMBTY320 Page 29
Result and Discussion:
LMBTY320 Page 30
Learning Outcome
To be filled in by Faculty
S. No. Parameter Marks Max. Marks
obtained
1 Understanding of the student about the 20
procedure/apparatus.
2 Observations and analysis including learning 20
outcomes.
3 Completion of experiment, Discipline and 10
Cleanliness.
4 Signature of Faculty.
LMBTY320 Page 31
Experiment 7
1. Experiment: Sequence Based Database Search and Gene prediction: BLAST
Equipment Required: Computer with internet connection.
2. Learning Objectives: To acquaint students with sequence based database similarity
search.
Students will learn to characterize novel sequences based on similarity and significance
of result.
3. Theory/Principle/Background of the topic: Basic Local Alignment Search Tool, or
BLAST, is an algorithm for comparing primary biological sequence information, such as the
amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST
search enables a researcher to compare a query sequence with a library or database of
sequences, and identify library sequences that resemble the query sequence above a certain
threshold. Different types of BLASTs are available according to the query sequences. For
example, for annotation of a previously unknown gene in the mouse, a scientist will typically
perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST
will identify sequences in the human genome that resemble the mouse gene based on similarity
of sequence.
4. Procedure:
1. Visit the website of online sequence based database search tool: BLAST.
2. Explore the different input options (e.g., type of BLAST, database option, scoring
scheme etc.).
3. Perform protein BLAST with default parameters.
4. Analyse the output (alignment score, e-value, database cross reference, positive,
identity, gaps etc.).
5. Change parameters e.g., BLOSUM, E value cut-off, masking option etc. Observe
influence on output.
6. For the same query protein, compare the protein sequence as well as coding nucleotide
sequence across database. Compare the results.
5. General calculations: Query subject identity (number of identical residues/length of
alignment) *100
LMBTY320 Page 32
6. Results:
Number of records obtained after performing search.
7. Scope of result: This experiment will predict relationships and homologies among
related species.
8. Results required: Parameter: word size.
9. Cautions: Hits to be evaluated based on score and E value.
Suggested Reading:
Books:
NCBI Handbook
LMBTY320 Page 33
Date of Performance Worksheet of the student Registration Number:
Aim:
Observations:
Calculations:
LMBTY320 Page 34
Result and Discussion:
LMBTY320 Page 35
Learning Outcome
To be filled in by Faculty
S. No. Parameter Marks Max. Marks
obtained
1 Understanding of the student about the 20
procedure/apparatus.
2 Observations and analysis including learning 20
outcomes.
3 Completion of experiment, Discipline and 10
Cleanliness.
4 Signature of Faculty.
LMBTY320 Page 36
Experiment 8
1. Experiment: Protein Structure Prediction Tool/Software: GOR
Equipment Required: Computer with internet connection.
2. Learning Objectives: To acquaint students with structure prediction tool for protein
sequences with unknown structure.
3. Theory/Principle/Background of the topic: The GOR method analyzes sequences to
predict alpha helix, beta sheet, turn, or random coil secondary structure at each position based on
17-amino-acid sequence windows. The original description of the method included four scoring
matrices of size 17×20, where the columns correspond to the log-odds score, which reflects the
probability of finding a given amino acid at each position in the 17-residue sequence. The four
matrices reflect the probabilities of the central, ninth amino acid being in a helical, sheet, turn, or
coil conformation. In subsequent revisions to the method, the turn matrix was eliminated due to
the high variability of sequences in turn regions. GOR method achieved higher efficiency
compared to ChouFasman because of its consideration of environment and flanking residues.
4. Outline of Procedure:
1. Visit the website of online Secondary structure prediction tool: GOR.
2. Take query protein sequence with unknown structure from sequence database.
3. Perform Secondary structure prediction.
4. Analyse the output (secondary structure elements and their arrangement).
5. General calculations: Secondary structure element percentage. (number of residues in
helix/total number of residues)*100.
6. Results:
Number of secondary structure elements predicted after performing analysis.
7. Scope of result: This experiment will give knowledge about secondary structure details
of proteins and their prediction method.
8. Results required: Parameter: Length of query.
9. Cautions: Structure prediction is not required for proteins with known structure.
Suggested Reading:
LMBTY320 Page 37
Websites:
http://gor.bb.iastate.edu/
LMBTY320 Page 38
Date of Performance Worksheet of the student Registration Number:
Aim:
Observations:
Calculations:
LMBTY320 Page 39
Result and Discussion:
Learning Outcome
LMBTY320 Page 40
To be filled in by Faculty
S. No. Parameter Marks Max. Marks
obtained
1 Understanding of the student about the 20
procedure/apparatus.
2 Observations and analysis including learning 20
outcomes.
3 Completion of experiment, Discipline and 10
Cleanliness.
4 Signature of Faculty.
LMBTY320 Page 41
Experiment 9
1. Experiment: Protein Structure Prediction Tool/Software: JPRED
Equipment Required: Computer with internet connection.
2. Learning Objectives: To acquaint students with structure prediction tool for protein
sequences with unknown structure.
3. Theory/Principle/Background of the topic: The JPRED method analyses sequences to
predict alpha helix, beta sheet or random coil secondary structure at each position based on
neural network, hidden markov model and position specific scoring matrix. It also predicts
coiled coil structure with lupas method. Solvent accessibility is calculated to measure the burial
status and reliability score is calculated. Reliability score 7 and above are considered significant
for predictions. UniRef90 is used as Reference database for making profiles and position
specific scoring matrix. Helices are represented by ‘H’, strands by E and coils/loops by ‘-‘.
4.
4. Outline of Procedure:
1. Visit the website of online Secondary structure prediction tool: JPRED4.
2. Take query protein sequence with unknown structure from sequence database.
3. Perform Secondary structure prediction.
4. Analyse the output (secondary structure elements and their arrangement), Jrel score,
Jnet25, Jnet5 etc.
5. General calculations: Secondary structure element percentage. (number of residues in
helix/total number of residues)*100.
6. Results:
Number of secondary structure elements predicted after performing analysis.
7. Scope of result: This experiment will give knowledge about secondary structure details of
proteins and their prediction method.
8. Results required: Parameter: Length of query.
9. Cautions: Structure prediction is not required for proteins with known structure.
Suggested Reading:
LMBTY320 Page 4
Websites:
http://www.compbio.dundee.ac.uk/jpred/
LMBTY320 Page 43
Date of Performance Worksheet of the student Registration Number:
Aim:
Observations:
Calculations:
LMBTY320 Page 44
Result and Discussion:
LMBTY320 Page 45
Learning Outcome
To be filled in by Faculty
S. No. Parameter Marks Max. Marks
obtained
1 Understanding of the student about the 20
procedure/apparatus.
2 Observations and analysis including learning 20
outcomes.
3 Completion of experiment, Discipline and 10
Cleanliness.
4 Signature of Faculty.
LMBTY320 Page 46
Experiment 10
1. Experiment: Protein Structure Prediction: Swiss
Model. Equipment Required: Computer with internet.
2. Learning Objectives: To acquaint students with the sequence analysis and tertiary
structure prediction tool.
3. Theory/Principle/Background of the topic: Homology modelling, also known as
comparative modelling of protein, refers to constructing an atomic-resolution model of the
"target" protein from its amino acid sequence and an experimental three-dimensional structure
of a related homologous protein (the "template"). Homology modelling relies on the
identification of one or more known protein structures likely to resemble the structure of the
query sequence, and on the production of an alignment that maps residues in the query
sequence to residues in the template sequence. It has been shown that protein structures are
more conserved than protein sequences amongst homologues, but sequences falling below a
20% sequence identity can have very different structure. SWISS-MODEL is a structural
bioinformatics web-server dedicated to homology modelling of protein 3D structures.
Homology modelling is currently the most accurate method to generate reliable three-
dimensional protein structure models and is routinely used in many practical applications.
Homology (or comparative) modelling methods make use of experimental protein structures
("templates") to build models for evolutionary related proteins ("targets").
4. Outline of Procedure:
1. Visit the website of online tertiary structure prediction tool: SWISS MODEL
2. Read about CASP and the citation section.
3. Perform tertiary structure prediction.
4. Analyse the output (secondary structure elements and their arrangement, fold of protein,
identification of related structures, RMSD value, Z value, QMEAN, QMEAN4 etc.).
5. General calculations: Template Target identity (number of identical residues/length of
alignment) *100
6. Results:
Number of models obtained after performing search and their energy.
7. Scope of result: This experiment will give information about how to predict protein
folds from sequence of protein.
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8. Results required: Parameter: QMEAN.
9. Cautions: Suitable template should be selected.
Suggested Reading:
Web address:
http://swissmodel.expasy.org/
LMBTY320 Page 48
Date of Performance Worksheet of the student Registration Number:
Aim:
Observations:
Calculations:
LMBTY320 Page 49
Result and Discussion:
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Learning Outcome
To be filled in by Faculty
S. No. Parameter Marks Max. Marks
obtained
1 Understanding of the student about the 20
procedure/apparatus.
2 Observations and analysis including learning 20
outcomes.
3 Completion of experiment, Discipline and 10
Cleanliness.
4 Signature of Faculty.
LMBTY320 Page 51
