Gaurav Arora

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Genomics at Georgetown University

Course Overview

GEP annotation projects were used in an indepenndent study with one student for the first time during Spring 2014. Weekly meetings were held with the student. At the beginning of the semester, the student learned the techniques of annotation using the simple annotation example. Later on in the semester, the student used the techniques from the first example and used evidence-based information to annotate contigs at higher levels. We started with the D. melanogaster contigs and were able to annotate D. biarmipes

Implementation

As mentioned earlier we started with a simple annotation problem example which used theD.melanogaster contig. As the semester progressed the weekly meeting discussions included discusssion of key concepts and going over few examples. The student would send regular reports via emails and report in person any issues with the actual annotation. A lot of the trouble shooting was done in person with help from the GEP support staff. By the end of the semester we submitted three contigs (contig 13, 19 and 70) from the D. biarmipes

Lessons Learned and Future Plans

During the semester the student was able to use the evidence-based tracks to annotate the gene co-ordinates. A lot of the annotation was available from the RNA-seq based evidence.This evidence was used in conjunction with evidence from other tracks. One lesson that was learned was to use as much evidence to make correct infrerences rather than base the annotation on a handful of evidences. 

We would like to annotate more contigs in the D. biarmipes

Syllabus for

In development - independent study