Readings & Practice Problems Help Center Learn more.

Welcome. Here is a list of readings and practice problems for the course. Many of the readings are associated with video lectures.

The practice problems are highly recommended. Hands-on experience is crucial in bioinformatics. The practice problems will help you become familiar with basic bioinformatics and answers are included at the end. I will also include optional supplemental readings for those who may want to learn more.

Week 5: Eukaryotic Gene Structure - July 8 - July 15

Assigned Reading
Single Nucleotide Polymorphism (reading goes with video lecture on Single Nucleotide Polymorphisms): PDF
Eukaryotic Gene Prediction (reading goes with video lecture on Eukaryotic Gene Structure): PDF
DNA Fingerprinting (reading goes with video lecture on DNA Fingerprinting): PDF
Ensembl (reading goes with video lecture on Ensembl database): PDF

Practice Problems
Practice Problems 1 - Gene Prediction, Fingerprinting: PDF
Practice Problems 2 - Ensembl, SNPs - PDF

Assignments
Week 5 Assignment (Auto Graded using Quiz mechanism): PDF  DOCX



Week 4: Bacterial Gene Structure - June 30 - July 7

Assigned Reading
Prokaryotic Genes, Promoters (reading goes with video lecture on Bacterial Genomes): PDF
Prokaryotic Gene Prediction (reading goes with video lecture on Bacterial Gene Finding): PDF
Viral Databases (reading goes with video lecture on Secondary Structure Prediction): PDF

Practice Problems
Practice Problems - Bacterial, Viral Genomes: PDF

Assignments
Week 4 Peer Assignment (see Peer Assessment on left menu): PDF  DOCX


Week 3: Protein Bioinformatics - June 23 - June 29

Assigned Reading
Motifs, Domains, Patterns (reading goes with both video lecture on Protein Motifs and video lecture on Prosite Patterns, Profiles): PDF
Molecular Weight, Isoelectric Point, Localization (reading goes with video lecture on Protein Predictions): PDF
Secondary Structure Prediction (reading goes with video lecture on Secondary Structure Prediction): PDF
Structure Databases, Structure Viewers (reading goes with video lecture on Protein Data Bank - PDB): PDF

Practice Problems
Practice Problems - Part 1: Pairwise Sequence Alignment: PDF
Practice Problems - Part 2: Protein Predictions/Secondary Structure: PDF
Practice Problems - Part 3: Protein Data Bank: PDF

Assignments
Week 3 Peer Assignment (see Peer Assessment on left menu): PDF  DOCX



Week 2: Biological Databases - June 16 - June 22

Assigned Reading
Introduction: What is BLAST and why do it?: PDF
Global & Local Alignment (reading goes with video lecture on Dynamic Programming): PDF
Substitution Matrices, Gap Penalties (reading goes with video lecture on PAM Matrices): PDF
Amino Acid Codes, Homology (reading goes with video lecture on Pairwise Sequence Alignment): PDF
BLAST (reading goes with YouTube video on BLAST): PDF
E Value Mathematics (reading goes with video lecture on E Values): PDF
PSI-BLAST, Delta-Blast (reading goes with video lecture on PSI-BLAST): PDF

Practice Problems
Practice Problems - Part 1: Pairwise Sequence Alignment: PDF
Practice Problems - Part 2: BLAST, FASTA: PDF
Practice Problems - Part 3: PSI-BLAST, Delta-BLAST: PDF

Assignments
Week 2 Peer Assignment (see Peer Assessment on left menu): PDF DOCX



Week 1: Biological Databases - June 9 - June 15

Assigned Reading
Basics/Language of Molecular Biology (designed for those with little biology background): PDF
Database Structures (reading goes with video lecture on Databases): PDF
PubMed (reading goes with video lecture on PubMed): PDF
NCBI Relational Database (reading goes with video lecture on the NCBI Sequence Database): PDF

Practice Problems
Practice Problems - Part 1: Molecular Biology and PubMed: PDF
Practice Problems - Part 2: NCBI Database: PDF

Assignments
Week 1 Assignment (use quiz tool to submit answers for auto-grade): PDF

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