Julia Emerson Amherst College
Gene Annotation at Amherst College
Gene annotation using GEP materials is done in the Biology 191 course (Molecules, Genes and Cells) at Amherst College. Biology 191 is one of two required introductory courses for the biology major at Amherst, and it is taken by many additional students to fulfill the pre-medical requirements. Class enrollment is 90-120 students each year, and the course is predominately made up of first-semester sophomores, due to a chemistry pre-requisite. There are three hours of lecture and an optional (4th hour) question and answer session each week. Each student also attends one of the three-hour lab sections each week, and lab enrollment is between 20 and 24 students per section. Students receive instruction and assistance in lab from one faculty instructor and two undergraduate teaching assistants. In 2011, gene annotation was done primarily in the lab periods during the last full, four weeks of the course, and lectures on gene structure and gene expression were completed just prior to the start of the annotation labs. Extra TA training sessions were held prior to the first and second weeks of the annotation labs.
2011 - Implementation
The goals of this four-week set of gene annotation labs were equally balanced between (1) involving large numbers of introductory biology students in a nationwide, collaborative research project; and (2) having students gain a richer understanding of eukaryotic gene structure and RNA processing than from lectures and problem sets alone. During the first week of gene annotation work, the Lab Coordinator (using Power Point slides and the GEP Web site) introduced all students in the course to the GEP research objectives during the Tuesday "4th hour" (which preceded all the labs for the week). The pre-lab reading assignment for the week was an Introduction to the GEP Collaborative Drosophila Annotation Research Project, which included revised parts of the GEP's Annotation Instruction Sheet. The lab instructor of each lab section provided a brief overview of BLAST to the students, who then worked through a revised version of the GEP's Simple Introduction to NCBI BLAST exercise. Most students worked individually at a desktop computer, but they were encouraged to talk with their neighbors/lab partner about what they were doing and learning. The TAs checked in with each student before he/she left lab for the day to make sure they had come up with correct answers to four new questions that we incorporated into the activity in 2011.
At the beginning of the next lab, the instructor displayed several Power Point-based "quiz" questions drawn from the "Introduction to the GEP" and the BLAST activity, and students jotted down answers on a blank answer sheet. This was an ungraded quiz and the lab instructor went over questions that were answered incorrectly by large numbers of students, to make sure that all students understood the particular topics addressed by those questions.1 Following the quiz discussion, students worked individually on a revised and expanded version of the GEP's A Simple Annotation Problem (renamed A Sample Annotation Problem). Students were once again encouraged to discuss the activity with their neighbors, and the lab instructor and teaching assistants circulated around the lab to answer additional questions. About an hour before the end of the lab period, all students took a short break from their individual work so that the lab instructor could explain to the group how to use the UCSC Genome Browser to do fine mapping of exon boundaries, including how to find reading frames, splice sites, and looking at + and – strand DNA sequences, all areas where students tend to get confused. Students then resumed their work, and each student was required to show his or her completed "Sample Annotation" worksheet to a teaching assistant before leaving lab for the day. Any students who did not finish the activity were instructed to complete it as homework.2
At the beginning of the third week, students selected (via a random draw) an isoform of a gene from fosmid(s) that had been pre-screened by the lab coordinator to determine which predicted features were likely to be real genes.3 The lab section's fosmid(s) were then projected on the large screen, and the lab instructor spent a few minutes going over information displayed in the UCSC Genome Browser window and how the selected gene features were identified. Two or more students in each lab section were assigned to genes with multiple isoforms, so that they could collaborate in completing the annotation. We also evened out the workload somewhat between student teams by assigning more than one pair of students to gene isoforms with ~12 or more exons. Students then proceeded to work on their selected isoforms using Amherst's How-To Guide for Gene Annotation4, parts of which refer students back to the "Introduction to the GEP" annotation overview and the “Sample Annotation Problem." Students working on the same gene were encouraged to collaborate to check their work and their gene models. Each TA held a one-hour help session over the weekend after this third week, so that students could ask questions and get one-on-one assistance with their individual projects.
In the fourth and final week, students completed work on their gene models. Students were given an Advanced Annotation Instruction Sheet (another modification of a GEP handout), which addressed particular sticking points that came up during the previous week. Each student created and submitted a Word document, which included a screen shot of the Gene Record Finder with the coding sequences of his/her particular isoform and the exon-by-exon BLAST searches, and also submitted an Annotation Report for his/her isoform.5 Any students who finished early were ‘deputized’ as TA’s to help their fellow students. A course tradition is to have pizza and soft drinks during the final lab, and we used part of this time to have students briefly comment on anything of particular interest about their gene model to the other students. The lab coordinator then compiled the individual isoform reports into fosmid reports after the semester ended.6
2011 - Lessons Learned and Future Plans
The following comments refer to the numbers in the above section.
1In the future, we may turn this into a pre-lab, online quiz, which will be automatically graded and provide us with more advance notice of which concepts are confusing to the students.
2An answer key to the Sample Annotation Problem is posted on the course Blackboard site at the end of the second week of annotation labs. Students can then compare their answers to the key, thereby reinforcing their understanding of annotation concepts and methodology.
3One problem in annotating many different, newly-sequenced genes in large enrollment courses is that each gene may present different challenges, and it is difficult to train all instructors and TAs for all possible scenarios. As a result, we have decreased the number of new features that students annotate each year and pre-screen all of them prior to the TA training sessions. In this way, we know what most of the challenges will be ahead of time and are better able to help students when they get confused.
4One caveat of providing the How-To Guide is that some students may be successful in following directions, but do not really understand what they are doing and why. Therefore, it is important that the instructional staff frequently ask students to explain the rationale for the specific steps as they work through the procedure.
5We have all students who work on the same isoform in each lab section submit one (joint) annotation report. We also have all the genes on each claimed fosmid annotated by students in two different lab sections, so that we can compare the two annotation reports to one another.
6Since most individual projects and gene models are not carefully checked until they are graded, the final annotation reports cannot be compiled until after the labs are over (in case any revisions/additions to particular models need to be made). Thus, the lab coordinator is ultimately responsible for compiling and submitting the final fosmid annotation reports and data files. We now limit the number of fosmids that are claimed, to reduce the workload of the lab coordinator (which is significant in a class of over 100 students!).
Gene Annotation in the 2012 Biology 191 Course
The number of weeks we devote to gene annotation ranges from four weeks (as described above) to just one week of laboratory work, as it depends in part upon the preferences of the faculty members who rotate through the Biology 191 course. In the one-week lab we developed in 2012, we de-emphasized the research objective of this work to focus on introducing students to bioinformatics tools while reinforcing concepts of eukaryotic gene structure, mRNA splicing and translation reading frames. Students work through a new worksheet that we created by combining and modifying parts of the GEP’s An Introduction to NCBI BLAST, the Sample Annotation Problem and the How-To-Guide. Students in each lab section work as a group to annotate the same gene and create a gene model (see the 2012 files linked below). Although students may miss out on the excitement of working on their “own” uncharted genes in the one-week lab, we believe that they are nonetheless gaining a richer understanding of eukaryotic gene structure and how to use on-line databases, which will serve them well in their upper-level biology course work, future research experiences and post-graduate studies in the biological or biomedical sciences.
Syllabus for Biology 191: Molecules, Genes and Cells
The Syllabus is available for download as a pdf file:
List of documents
- 2012 Bio 191 Annotation Report
- 2012 Completed Bio 191 Annotation Report for yellow-h
- 2012 Annotation Lab
- 2012 Annotation Lab Answer Key
- Introduction to NCBI BLAST
- Answers to BLAST Activity
- BLAST Quiz (Questions, Blank Answer Sheet)
- Introduction to the GEP Collaborative Research Project
- Introductory Power Point Slides
- Sample Annotation Problem
- Answers to Sample Annotation Problem
- Helpful Annotation Tips
- How-To Guide for Gene Annotation
- Advanced Annotation Instruction Sheet