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Fundamental Models and Algorithms in Bioinformatics

INFO I519 (= I617) Fall 2021


Course description

INFO I519 FMAB

Class times and locations

Mon, Wed 3:15p - 4:30p (Credits: 3.0); Lindley Hall (LH) 025
Computer Laboratory, Fri 9:25a - 10:40a; Radio-TV (TV) 186

Tentative schedule (class notes can be viewed with Adobe Acrobat Reader)

btn_printerFriendly.gif version of this schedule

DAYDATELECTURETOPICLECTURER
Mon Aug 23 1.1 Orientation

Topics in bioinformatics, scope of class, and resources

Catch-up for non-life scientists: An introduction to DNA (Khan Academy)

Module 1: Bioinformatics resources and workspaces



National Center for Biotechnology Information (NCBI), a great starting point for "anything" bioinformatics

Ubuntu on Windows: ... a quick way to get to a command line terminal

Virtual Machines: VirtualBox VMware

Volker Brendel
Wed Aug 25 1.2 Basic bioinformatics toolkit acquisition (Part I)

NCBI E-Utilities
... slides
Installing NCBI EDirect
EDirect Sample Code Explained

Volker Brendel
Fri Aug 27 L1.1 Computer Laboratory: Linux Basics

Basic UNIX shell tutorial
The UNIX Shell
The UNIX Shell: Summary of Basic Commands
vi(m) editor tutorial

Shivani Vogiral
Mon Aug 30 1.3 Mapping biological question onto computational problems:
The modeling spiral

Sequence gazing: the famous TATA-box

Volker Brendel
Wed Sept 1 1.4 Basic statistical questions in bioinformatics


Quiz I
Volker Brendel
Fri Sept 3 L1.2 Computer Laboratory: Basic bioinformatics toolkit acquisition (Part II):

Getting code: git GitHub Brendel Group on GitHub

GitHub HowTo
git: working with branches
CodeFMAB
Shivani Vogiral
Mon Sept 6 2.1

Module 2: Sequence Models and Spaces



Labor Day

no class
Wed Sept 8 2.2 Simple Sequence Models Volker Brendel
Fri Sept 10 L2.1 Computer Laboratory: Python Basics

Python tutorial
Python Scripting for Computational Molecular Science
Python for Everybody PY4E Lessons
J. Sundnes: Introduction to Scientific Programming with Python

Style matters ...
Learning Scientific Programming with Python - an intriguing resource

Shivani Vogiral
Mon Sept 13 2.3 Markov Models for Sequences

Volker Brendel
Wed Sept 15 2.4 Applications of Markov Models

GENMARK

Some resources for statistics background review:
Event probabilities
Union of events
Bayes Theorem
Probability distribution
Expected value
Review: Conditional Probability
Sensitity, specificity, and all that

Stat225 at Purdue - nice slides by Dr. Whitney Huang


Quiz II
Volker Brendel
Fri Sept 17 L2.1 Computer Laboratory:

Coding random sequence generation and pattern probability calculations
Shivani Vogiral
Mon Sept 20 3.1

Module 3: Pairwise Sequence Alignment





Models for Pairwise Sequence Alignment

Volker Brendel
Wed Sept 22 3.2 PWSA: #NW algorithm. Volker Brendel
Fri Sept 24 L3.1 Computer Laboratory: Coding #NW algorithm. Shivani Vogiral
Mon Sept 27 3.3 Algorithms for Pairwise Sequence Alignment

How Do We Compare Biological Sequences?
(from Bioinformatics: An Active Learning Approach)
Volker Brendel
Wed Sept 29 3.4 PWSA: gSW, lSW, and other algorithms. Volker Brendel
Fri Oct 1 L3.2 Computer Laboratory: Coding PWSA algorithms.

Quiz III to be posted as an assignment.
Shivani Vogiral
Mon Oct 4 4.1

Module 4: Sequence Analysis with Scores





Sequence Analysis with Scores: Theory
Volker Brendel
Wed Oct 6 4.2 Sequence analysis with scores: Substitution scoring matrices
Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis)

NCBI BLAST

slides for Sequence Analysis I presentation
handout for Sequence Analysis I presentation

NCBI BLAST download site
Volker Brendel
Fri Oct 8 Fall Break: no class
Mon Oct 11 4.3 Sequence Analysis with Scores: Applications

Volker Brendel
Wed Oct 13 4.4 TBA

Quiz IV
Volker Brendel
Fri Oct 15 L4.2 Computer Laboratory: Shivani Vogiral
Mon Oct 18 5.1

Module 5: Hidden Markov Models





Hidden Markov Models: Motivation

Rabiner's Tutorial
Volker Brendel
Wed Oct 20 5.2 Hidden Markov Models: Algorithms

Hidden Markov Models
(from Bioinformatics: An Active Learning Approach)
Volker Brendel
Fri Oct 22 L5.1 Computer Laboratory: Plotting functions and histograms and more with python Shivani Vogiral
Mon Oct 25 5.3 Hidden Markov Models: Applications

Application examples
GENSCAN
Profile Hidden Markov Models
TagDust Tagdust2 on github

Volker Brendel
Wed Oct 27 5.4 Sequence motifs: algorithms

InterPro
The MEME Suite
HOMER

Quiz V posted
Volker Brendel
Fri Oct 29 L5.2 Computer Laboratory: Implementation of HMM algorithms Shivani Vogiral
Mon Nov 1 6.1

Module 6: Basic Concepts of Molecular Phylogenetics





Molecular Phylogeny: Models

The powers and pitfalls of parsimony
Volker Brendel
Wed Nov 3 6.2 TBA Volker Brendel
Fri Nov 5 L6.1 Computer Laboratory: Molecular Phylogeny, applications Shivani Vogiral
Mon Nov 8 6.3 Molecular Phylogeny: Applications

Lectures on molecular phylogeny
(from Bioinformatics: An Active Learning Approach)
Volker Brendel
Wed Nov 10 6.4 TBA

Quiz VI
Volker Brendel
Fri Nov 12 L6.2 Computer Laboratory: Shivani Vogiral
Mon Nov 15 7.1

Module 7: Genome Assembly and Annotation





DNA Sequencing
Sanger sequencing
Illumina sequencing
nanopore sequencing

Genome Resources
The Genomic Landscape circa 2016 (Lecturer: Dr. Andy Green)

Assembly basics
NCBI Assembly Help
NCBI Genome

Genome Assembly
Introduction to genome sequencing
How do we assemble genomes?
from Bioinformatics Algorithms: An Active Learning Approach

Volker Brendel
Wed Nov 17 7.2 Protein Structures
RCSB PDB

PDB: What is a protein?
PDB: How enzymes work

peptide bond
Ramachandran plot ... very nice visualization thereof
(thanks to Prof. Eric Martz)

Guide to PDB

PDB Molecule of the Month
NCBI Protein

Protein bioinformatics: structure prediction

Nobel Price lecture 2013: Michael Levitt

foldit

Project Assignment Posted
Volker Brendel
Fri Nov 19 L7.1 Computer Laboratory: Shivani Vogiral
Mon Nov 23 THANKSGIVING BREAK n/a
Wed Nov 25 THANKSGIVING BREAK n/a
Fri Nov 27 THANKSGIVING BREAK n/a
Mon Nov 29 8.1

Module 8: Genetic Variation





Genetic variation
Interpreting an individual genome

NCBI dbSNP    How To
NCBI dbVar    How To
1000 Genomes Project    Nature 491:56
Example: rs1131769

file format specifications:

Variant Call Format (VCF)
Sequence Alignment Map format (SAM)
SAM flags explained
Pileup format (used by samtools)


Relevant code:

NCBI SRA Toolkit
samtools
bwa
freebayes
Volker Brendel
Wed Dec 1 9.1

Module 9: Protein Structure





peptide bond
Ramachandran plot ... very nice visualization thereof
(thanks to Prof. Eric Martz)

PDB: What is a protein?
PDB: How enzymes work
HIV I
HIV II

Guide to PDB

PDB Molecule of the Month
NCBI Protein

Secondary Structure

2struct server

Jpred - secondary structure prediction
SPIDER3

foldit
AlphaFold
Volker Brendel
Fri Dec 3 L7.2 Computer Laboratory:

wgsim - read generator
SoapDeNovo2 - assembler

Project Assignment Due
Shivani Vogiral
Mon Dec 6

Review Sessions



Sequence Alignment

Bioinformatics Algorithms presentation
Volker Brendel
Wed Dec 8 Gene Expression Analyses
from Bioinformatics Algorithms: An Active Learning Approach

MIT Lecture: Gene Regulatory Networks
MIT Data Science: Clustering
Volker Brendel
Fri Dec 10 Zoom office hour Shivani Vogiral
Mon Dec 13 12:35 - 2:35pm Final Examination Students