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Gene Annotation

Quick Check of Student Annotations

This document describes a protocol that GEP faculty can use to quickly identify potential errors in student gene annotations.

Analysis of a Chimp Chunk

Following the step-by-step tutorial “Chimp BAC Analysis: Genes and Pseudogene”, students should be ready to annotate a chunk of chimpanzee DNA themselves, presenting evidence to support their claim of a gene or pseudogene. An example student report from the Bio 4342 course at WU is available here.

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.

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.

GenBank Accession Number Reference Sheet

This document describes the naming conventions used by NCBI. Students can use these naming conventions to quickly evaluate the type and the reliability of the sequences in the NCBI database.

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.