NCBI Bioinformatics Mini-Courses: November 8-9

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The MIT Libraries will sponsor a series of 4 NCBI bioinformatics mini-courses on, November 8-9, 2007 in the Hayden Library DIRC, 14N-132. Each course is 2.5 hours in length, including a lecture followed by a 1-hour hands-on session. There is no advance registration but space is limited. There are computers for 20 attendees, plus space for 10 attendees with their own laptops.

Contact Louisa Worthington Rogers with questions.

Thursday, November 8:

9:30am-12:00pm – Microbial Genomes Quickstart (New class!)

In this mini-course, you will learn how to access the microbial genome sequences and annotations, how to navigate through and download the gene and protein datasets, and will be introduced to the available genomic and comparative genomic analysis tools. The course will address practical discovery questions such as ‘Are there identifiable genes in microbial genomes that may be horizontally transferred?’ and ‘What are the differences between closely-related pathogenic and non-pathogenic bacteria?’

1:00pm-3:30pm – Mapviewer Quick Start

In this course, we will use the human genome Map Viewer. Used to view the NCBI assembly of the complete human genome, Map Viewer is a valuable tool for the identification and localization of genes that contribute to human disease. In this course, we will see how to view different human genome maps and make best use of them. We will learn to locate a human gene, download its sequence along with its upstream sequence (to analyze promoter regions), obtain exon-intron coordinates, find a possible splice variant and identify whether the variations in the gene are associated with a disease.

Friday, November 9:

9:30am-12:00pm – Structural Analysis Quick Start

This course covers how to visualize and annotate 3D protein structures using NCBI’s Cn3D, identify conserved domain(s) present in a protein, search for other proteins containing similar domain(s), explore a 3D modeling template for the query protein and find distant sequence homologs that may not be identified by BLAST.

1:00pm-3:30pm – Making Sense of DNA and Protein Sequences

In this mini-course, we will find a gene within a eukaryotic DNA sequence. We will then predict the function of the implied protein product by seeking sequence similarities to proteins of documented function using BLAST and other tools. Finally, we will find a 3D modeling template for this protein sequence using a Conserved Domain Database Search.

About the Instructors:

Medha Bhagwat and Steve Pechous are biologists on the User Services staff of the National Center for Biotechnology Information.