Primer on Reading Frames and Phase
This primer provides an overview on how to determine the phase of donor and acceptor splice sites.
Home » Gene Annotation »
Gene Annotation
Web Databases for Drosophila
This PowerPoint presentation introduces the species-specific databases available on the web, including FlyBase and the Ensembl Drosophila melanogaster database.
About Synteny Analysis
A one-page summary of the logic process used to determine if genes in a fosmid are syntenic with respect to D. melanogaster
Quick Check of Student Annotations
This document describes a protocol that GEP faculty can use to quickly identify potential errors in student gene annotations.
Chimp Chunk Projects without Student Reports
Additional chimp chunk projects without student reports. Please contact Dr. Chris Shaffer for instructions on how to create additional chimp annotation projects.
Sample Chimp Chunk Reports
Three sample chimp chunk projects with student reports.
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.
Guidelines for your Chimp Chunks Report
Brief guidelines with advice on annotating chimpanzee DNA, including what to put in the final report.
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.