Introduction to Bioinformatics

APHL Annual MeetingBioinformatics Platform Options for Public Health LaboratoriansJune 3 2019Dr. Kelly F. Oakeson

Bioinformatics

• Sequence analysis

• Gene & protein expression

• Analysis of cellular organization

• Structural bioinformatics

• Databases

• Algorithm Development

• Software & tools

• Others?

Gene & protein expression

• Gene expression (RNA-Seq)

• Protein expression

• Analysis of regulation

Databases

• Biological sequence analysis: Genbank, UniProt

• Structure analysis: Protein Data Bank (PDB)

• Finding Protein Families and Motif Finding: InterPro, Pfam

• Next Generation Sequencing: Sequence Read Archive

• Network Analysis: Metabolic Pathway Databases (KEGG, BioCyc), Interaction Analysis Databases, Functional Networks

• Antimicrobial Resistance: The Comprehensive Antibiotic Resistance Database (CARD), National Database of Antibiotic Resistant Organisms (NDARO)

• Virulence Factors: The virulence factor database (VFDB)

Algorithm & Software Development

• Foundations in Discrete mathematics, control theory, system theory, information theory, and statistics

• Graph theory, artificial intelligence, soft computing, data mining, image processing, and computer simulation

• Open Source

• Commercial

Sequence analysis

• DNA sequencing

• Sequence assembly

• Genome annotation

• Computational evolutionary biology

• Comparative genomics

Command Line (CLI) vs. Graphical User Interface (GUI)

Vs.

Command Line (CLI) vs. Graphical User Interface (GUI)

Vs.

Graphical User Interface (GUI)

Graphical User Interface (GUI)

Graphical User Interface (GUI)

Graphical User Interface (GUI)

Graphical User Interface (GUI)

Command Line (CLI)

Command Line (CLI)

Command Line (CLI)

Command Line (CLI)

Command Line (CLI)

Command Line (CLI)

Command Line (CLI)

Command Line (CLI)

Command Line (CLI)

Command Line (CLI)

Command Line (CLI)

Command Line (CLI)

https://github.com/stephenturner/oneliners

Questions/Discussion