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Intermediate Student

Chimp BAC Analysis: Genes and Pseudogene

A step-by-step tutorial that takes the student through a gene identification problem in a chimpanzee BAC sequence using predictions from a gene prediction program (Genscan), the UCSC Browser and BLAST.

Browser-Based Annotation and RNA-Seq Data

This exercise continues your introduction to practical issues in comparative annotation. You will be annotating genomic sequence from the dot chromosome of Drosophila mojavensis using your knowledge of BLAST and some improved visualization tools. You will also consider how best to integrate information from high-throughput sequencing of expressed RNA.

Using mRNA and EST Evidence in Annotation

This exercise allows students to learn how to use mRNA and Expressed Sequence Tags (ESTs) evidence to assist their annotation efforts. An answer key is available for instructors.

Detecting and Interpreting Genetic Homology

An introductory exercise using BLAST to annotate a region in the Drosophila melanogaster genome. Students can use this exercise to gain familiarity with performing BLAST searches and interpreting BLAST output. An answer key is provided for instructors.

Introduction to ab initio and Evidence-based Gene Finding

This PowerPoint presentation examines the use of gene prediction programs (such as Genscan) in annotation, noting some of the limitations of gene prediction programs in creating putative gene models. It also introduces the UCSC and other browsers as sources of supporting evidence.

Design and Use of RepeatMasker

Similar to the lecture notes on Repetitious DNA, this is a PowerPoint presentation given by Dr. Jeremy Buhler for the GEP faculty and TA workshops. This presentation covers the basics of RepeatMasker, as well as limitations of the program that students should be aware of.

Using BLAST for Genomic Sequence Annotation

Similar to the Lecture Notes on Alignment, this is a PowerPoint presentation given by Dr. Jeremy Buhler for the GEP faculty and TA workshops. This presentation covers the basics of alignment, essential for students to correctly interpret BLAST results.