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Incorporating genome annotation with the Genomics Education Partnership (GEP) in an undergraduate biochemistry course
Author(s) -
Bednarski April Elaine
Publication year - 2013
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.27.1_supplement.838.11
Subject(s) - annotation , genome project , genome , genome browser , curriculum , computational biology , kegg , genomics , general partnership , personal genomics , biology , bioinformatics , genetics , gene , transcriptome , psychology , pedagogy , gene expression , finance , economics
A computer‐based lab was developed to accompany the second semester of a year‐long biochemistry sequence. The goal for this lab was to emphasize the importance of computers in modern biochemical research. Lecture covered signaling, metabolic pathways, and genome structure and organization. Students began by using the bioinformatics programs BLAST, OMIM, and KEGG, to analyze the impact of a DNA mutation on protein structure and function in a biochemical pathway. In the second module students learned about microarrays through research articles and online curriculum from GCAT ( www.bio.davidson.edu/gcat ) then worked with a microarray data set. The third module on genome annotation spans the final eight weeks of the laboratory. This module used curriculum generated by the GEP ( www.gep.wustl.edu ) and included three weeks of introduction to the UCSC Genome Browser and FlyBase followed by four weeks of annotating raw sequence data from Drosophila and a week of project presentations. During this module, students received data and had access to tools from the GEP. Assessment results indicate that students had a better understanding of how computers are used in biochemical research, gained understanding of genome organization, and enjoyed the collaborative nature of the genome annotation research project.