C5

Pandemic Flu Genomics Exercise

Dr. Robert Moss (Wofford College) has developed an annotation exercise on Influenza viruses.

Gene Annotation of Genomic DNA

Dr. James Bedard with students Amber Harlan and Joshua Machone presented a walkthrough on their annotation projects for a lunchtime talk series at Adams State College.

FlyBase for Undergrads

Dr. Hui-Min Chung (University of West Florida) and her students have developed an instructional video aimed at introducing undergraduate students to the research tools available at FlyBase.

Module TSS4: Annotation of Broad Transcription Start Sites

This module illustrates the use of computational (e.g., blastn) and experimental (e.g., RAMPAGE, CAGE, RNA PolII ChIP-Seq) data to define the narrow and wide TSS search regions for genes with broad promoters.

Module TSS3: CAGE, RAMPAGE, and RNA Pol II X-ChIP-Seq

This module uses the placement of the Initiator (Inr) motif, TSS annotations produced by the Celniker group at modENCODE, and experimental data such as CAGE, RAMPAGE, and RNA Polymerase II X-ChIP-Seq data to characterize the promoter for the Antp gene in D. melanogaster.

Module TSS2: Using Sequence Alignment to Identify a TSS

This module illustrates how pairwise (blastn) and multiple sequence alignments can be used in conjunction with RNA-Seq data and the Short Match functionality of the UCSC Genome Browser to facilitate the TSS annotation of the Antp gene in D. eugracilis.

Module TSS1: Transcription Start Sites Introduction

This module describes how Celniker TSS annotations, DNase I hypersensitive sites, and the 9-state chromatin models can be used in the classification of promoter shape for the Antp gene.

Module 6. Alternative splicing

This module explores how multiple different mRNAs and polypeptides can be encoded by the same gene. After completing this module students will be able to explain how alternative splicing of a gene can lead to different mRNAs and illustrate how alternative splicing can lead to the production of different polypeptides and result in drastic changes in phenotype.

Module 5. Translation: The need for an Open Reading Frame

In this module students will learn how mRNA is translated into a string of amino acids. After completing this module students will be able to determine the codons for specific amino acids as well as start and stop codons. They will be able to identify open reading frames for a given gene, define the phases of splice donor and acceptor sites and describe how they impact the maintenance of the open reading frame.