Bioinformatics: Algorithms and Applications

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NPTEL

Bioinformatics: Algorithms and Applications

Course Instructor: Prof. Michael Gromiha, IIT Madras

Date: 29 Jan 2022

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I’m Fathima Ridha Research scholar at IITM and “TA” for this course

HI!

Email: fathima.ridha.97@gmail.com

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POLL

Have you attempted Assignment 1?

• Yes

• Not Yet

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Course Details

Duration

12 weeks

24 Jan 2022 - 15 Apr 2022 Exam: 24 Apr 2022 IST

Pre-Requisites

Basic Biology and any computer

language

Level

Undergraduate/

Postgraduate

Biological Sciences

& Bioengineering, Computational

Biology

Course layout

Week 1 Introduction, DNA sequence analysis, DNA Databases

Week 2 Protein structure and function, protein sequence databases, sequence alignment

Week 3 PAM matrix, Global and local alignment, BLAST: features and scores Week 4 Multiple sequence alignment, Conservation score, phylogenetic trees Week 5 Protein sequence analysis, hydrophobicity profiles, non-redundant datasets Week 6 Protein secondary structures, Ramachandran plot, propensity, secondary

structure prediction

Week 7 Protein tertiary structure, PDB, visualization tools, structural classification, contact maps

Week 8 Protein structural analysis, protein structure prediction

Week 9 Protein stability, energetic contributions, database, stabilizing residues, stability upon mutations

Week 10 Protein folding rates, proteins interactions, binding site residues Week 11 Computer aided drug design, docking, screening, QSAR

Week 12 Development of algorithms, awk programming, machine learning techniques, applications using WEKA

Reference Book

M. Michael Gromiha, Protein Bioinformatics:

From Sequence to Function, Academic Press,

2010

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CERTIFICATE

CRITERIA TO GET A CERTIFICATE

Average assignment score = 25% of average of best 8/12 assignments Exam score = 75% of the proctored certification exam score out of 100 Final score = Average assignment score + Exam score

YOU WILL BE ELIGIBLE FOR A CERTIFICATE ONLY IF AVERAGE ASSIGNMENT SCORE >=10/25 AND

EXAM SCORE >= 30/75

If one of the 2 criteria is not met, you will not get the certificate even if the Final score >= 40/100.

• Certificate will have your name, photograph and the score in the final exam with the breakup and have the logos of NPTEL and IITM

• It will be e-verifiable at nptel.ac.in/noc

INTERNSHIP WITH FACULTY FOR COURSE TOPPERS!

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POLL

AUDIENCE STATS

• UG student

• PG student

• PhD scholar

• Teacher

• Industry

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POLL

REASON FOR TAKING THE COURSE

• Credit transfer via college

• Exploring new domain of knowledge

• Helpful for my job

• Mandated by college

• Someone suggested to enroll

• For GATE preparation

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Workflow of the most important methods and applications of bioinformatics technologies on COVID-19.

Ma, Lifei et al. “Comprehensiveanalyses of bioinformatics applications in the fight against COVID-19 pandemic.”Computational biology and chemistryvol. 95 (2021):

107599. doi:10.1016/j.compbiolchem.2021.107599

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Bioinformatics

“The mother and father of bioinformatics”

Margaret Oakley Dayhoff

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Bioinformatics as a Career

IT companies Research

institutes

Research associate Research scholar

Professor Data Analyst

Programmer Software developer

Pharma- biotech companies Pharmacologist

Scientist Analyst

01 02 03

Many more…..

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WEEK 1 Lec 1

• Definition of bioinformatics

• Major aspects

• Applications

Lec 2

• DNA Sequence analysis

• Sequence based Parameters

Lec 3

• Database

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Assignment Quiz

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Now for some numbers…

a. How many different types of nucleotides are found in RNA?

b. How many different types of amino acids are found in proteins?

c. How many nucleotides are needed to code for a single amino acid?

d. How many different codons are there in the genetic code?

e. How many codons code for amino acids?

Quiz ??

4

20

3

64

61

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Task

1. Using EMBOSS, find the complementary strand for the sequence:

CTCGGATTTGTAAAGATCATGATCTCATACATAGTACCTAGCCATTG (https://www.bioinformatics.nl/cgibin/emboss/)

2. Calculate the AT and GC content of the sequence AAATGGCCCTAA using Seq2Feature tool (https://www.iitm.ac.in/bioinfo/SBFE/compute_dna.html#tab-1-3)

3. How many “Homo sapiens” sequences deposited in DDBJ? Compare with Genbank and EMBL

4. Find the papers published by any author (E.g) Gromiha MM. in PubMed

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Bioinformatics: Algorithms and Applications

NPTEL