4. Comparative Genomics
To fully exploit the potential of this activity, the fourth exercise compares the presence of the identified gene or genes, their genomic
context, and their occurrence across different taxa. Using MaGe, a
robust comparative genomics platform (Vallenet et al., 2006), the
students further confirm the identity and putative function of the
gene(s) determined during the BLAST search. Student might ask,“Is
there any evolutionary relationship to explain the occurrence of the studied genes across different taxa?”
4.1. Access MicroScope website: https://www.genoscope.cns.fr/
4.2. Choose Escherichia coli K12 and select Load into genome
4.3. To identify the gene, search for “lacI” and click Move to.
4.4. Identify lacI gene putting the mouse over each red bar.
4.5. Select options menu.
4.6. In the new window opened, look for the section Viewer
Comparative Map default and choose synteny.
4.7. In the section PkGDB Organism Synteny, press the button
CTRL and choose Bacillus anthracis, another Escherichia species,
Salmonella bongori, Shigella sonnei, and Vibrio cholera.
4.8. Click Save options.
4.9. Compare the presence and the function of the gene in different taxa (Figure 4).
Learning objectives. Through this simple comparative genomics analysis, students learn
• to localize their target gene(s) within the chromosome,
• to identify the genomic features of the flanking regions,
• to determine gene homologies with selected taxa, and
• concepts such as synteny, homology, insertions, deletions, and
horizontal gene transfer.
The pilot trial showed that Internet access was not a limitation when
implementing these activities at schools. Nevertheless, teachers
could easily choose to exclude one of the exercises or, alternatively,
to challenge the students to carry them out as homework, and later
resume the bioinformatics exercises in the classroom.
Ana Sofia Martins is supported by a fellowship from Fundação para a
Ciência e Tecnologia – FCT (SFRH/BD/112038/2015). The authors
are grateful to all the participant schools and school teachers for
the opportunity to implement the bioinformatics exercises detailed
in this work, which contributed to improving the described activity.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990). Basic
local alignment search tool. Journal of Molecular Biology, 215, 403–410.
Bloom, M. (2001). Biology in silico: the bioinformatics revolution. The
American Biology Teacher, 63, 397–403.
Figure 4. Comparative genomics analysis carried out using MaGe. The genes and corresponding reading frames (+3, +2, +1, −1,
−2, −3) of the query genes are shown at the top. Below is an outline of other bacteria with which the query gene(s) are being