Sequences and Structures: An Introduction to Key Bioinformatics Tools

For more information or to schedule this course, please contact Jennifer Lyon <jennifer.a.lyon@stonybrook.edu>.

This face-to-face course will provide a basic introduction to accessing bioinformatics databases and tools and focus specifically on how to use two key techniques: sequence similarity searching and molecular structure viewing. Participants will learn how to locate high-quality bioinformatics resources online with a specific focus on knowledge of the key entry points into the National Center for Biotechnology Information's complex set of resources. Next, participants will learn how sequence similarity searching works, as distinct from any other type of searching, and gain a deeper understanding of how the highly popular Basic Local Aligment Sequence Tool (BLAST) programs function. Finally, participants will be introduced to the methods by which the molecular structures of proteins are analyzed, the two primary databases that contain these structures, and the NCBI's free software, Cn3D, that allows viewing and manipulation of the structures. Each section will include hands-on exercises. This course requires the attendee to have a basic knowledge of molecular biology concepts and terminology. Registered attendees will be provided with some reading material in advance on these topics.

Learning Objectives

Participants will be able to locate bioinformatics resources and tools.
Participants will be able to navigate the NCBI website and utilize key entrance points such as Entrez Gene, Taxonomy, and Entrez Nucleotide.
Participants will understand how sequence similarity searching differs from other database searching.
Participants will understand how the BLAST sequence similarity searching algorithms function for both nucleotide and protein sequences. Participants will be able to choose an appropriate BLAST program and manipulate the parameters of a BLAST Search.
Participants will be able to locate and search molecular structure databases: PDB and MMDB.
Participants will be able to use the Cn3D viewer to visualize molecular structures.
Participants will understand how structure similarity searching differs from other searching methods and how VAST, specifically, works. Participants will be able to compare molecular structures from VAST results in Cn3D.

Agenda

8am Introduction

8:15am - 9am Introduction to Bioinformatics Resources Lecture

9am-9:30am Hands-On Exercises

9:30-10am Start BLAST sequence similarity searching lecture

10am-10:15am Break

10:15am-11:30am Continue BLAST sequence similarity searching lecture and demonstration

11:30am-Noon Hands-On Exercises

Noon-1pm Lunch Break

1pm - 2:20pm Molecular Structure Viewing lecture and demonstration

2:20-2:55 pm Hands-On Exercises

2:55-3pm Wrap up/evaluations

Facility Requirements

A computer classroom with internet connectivity; projection capability for the instructor station.

MLA CE Credits: 6

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