Gene Annotation

Introduction to the Complete GEP Gene Annotation Process

Developed by Dr. Ken Saville (Albion College) and Dr. Gerard McNeil (York College, City University of New York), this walkthrough provides a comprehensive overview of the entire GEP gene annotation process. This walkthrough includes a brief description of the research problem and step-by-step instructions on how to use the UCSC Genome Browser, FlyBase, the Gene Record Finder and NCBI BLAST to investigate a feature in a Drosophila erecta Muller F element annotation project. The walkthrough then shows how students can use the Gene Model Checker to verify a gene model; it also includes a sample GEP Annotation Report.

Introduction to BLAST using Human Leptin

Dr. Justin R. DiAngelo (Penn State Berks) and Dr. Alexis Nagengast (Widener University) have developed an exercise that introduces students to the basic functionality of the NCBI web site and NCBI BLAST. Students will use NCBI BLAST to identify the putative orthologs of the human Leptin gene in other species.

Using BLAST and ExPASy for Genetic and Protein Analysis of H1N1 Variability

Ms. Julie Ertmann (University City High School, MO) has designed a standalone activity using BLAST for AP or second year high school biology students. This exercise uses BLAST and ExPASy for genetic and protein analysis of H1N1 variability, including mutations that confer resistance to antiviral medications. Development of this exercise was supported by an NSF Mathematics and Science Partnership grant #06344780, to B Schaal, Washington University in St. Louis. If you have questions about this activity, please email the author at:

Investigating a Mutation in HIV-1

Students use the HIV Problem Space on the BioQuest BEDROCK Website to investigate whether a specific HIV mutation can be correlated with a decline in immune system function. In order to perform this analysis, students must generate and analyze multiple sequence alignments of HIV sequences generated from the ALIVE study.

Identify D. melanogaster Ortholog

This decision tree illustrates the list of criteria that can be used to determine the putative D. melanogaster ortholog of a predicted gene.

GEP Annotation Workflow

This workflow provides an overview of the key analysis steps and bioinformatics tools for the annotation of a predicted gene in the Drosophila F element GEP project.

TSS Annotation Workflow

This workflow provides an overview of the key steps and recommended search parameters for the annotation of transcription start sites.

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.