Transcript Module 2: T-COFFEE & Module 8: Horizontal Gene Transfer

Lab Reports
Wrapping up IMG-ACT Genome Annotation
• Online notebook should be completed for all 3 genes
• Final reports are comprised of the imgACT online reports (one for
each gene) and a team summary of the project
– Each student on the team should complete the online reports for all 3
assigned genes. The reports must be printed out and turned in with your
team project summary & cover page.
– Each team should collectively summarize the results of their annotation
project. The summary must be printed out and one copy turned in to your
T.A., together with individual reports for each gene.
• DUE DATES
Wrapping up IMG-ACT Genome Annotation
Provide a COVER PAGE for your report:
Include your team name as well as the full names (and UIDs) of student
team members.
Include a LIST of the pathways or cell structures assigned to your team.
(some teams have only one while others have two).
Include a LIST of the gene OIDs that were annotated as part of this report.
Online Reports
Access REPORT from
team coursework page.
“Click” on the link under
step name column.
Online Reports
For each module,
enter requested
results in report
(from notebook).
Note that this format
is compatible for
eventual upload to
IMG database.
Online Reports
Skip Module 9 –
we did not annotate
RNA molecules
Note: Surmised from the analysis of data from ALL modules.
CLICK
when
finished
Online Reports
PRINTING your report: Delete “edit” from URL then press [Enter]
Online Reports
 Notice entry boxes have
been removed.
 Select [Print] from
drop-down menu.
 Include hard copy with
team report.
Team Project Summary
Include a graphical representation of your pathway or cellular structure,
highlighting genes annotated by team, as well as a summary table
ABC Transport Systems in
Planctomyces limnophilus DSM 3776
EX: CELLULAR STRUCTURE
Corresponding gene in P. limnophilus
Reference
Gene
Reference
Organism
Gene OID
(P. limnophilus)
SSuA
Rhodopirellula
baltica
2500607282
ABC-type nitrate/sulfonate/bicarbonate
Transport system, periplasmic component
SSuC
Rhodopirellula
baltica
2500607283
ABC-type nitrate/sulfonate/bicarbonate
Transport system, permease component
SSuB
Escherichia coli
ATCC 8739
2500607284
ABC-type nitrate/sulfonate/bicarbonate
Transport system, ATPase component
Proposed Gene Annotation
Team Project Summary
EX: PATHWAY
Corresponding gene in P. limnophilus
Reference
Organism
Gene OID
(P. limnophilus)
1.7.99.4
Rhodopirellula
baltica
2500607069
narB; nitrate reductase catalytic subunit
1.7.1.4
Rhodopirellula
baltica
2500606476
nitrite reductase (NAD(P)H) large subunit
6.3.1.2
Rhodopirellula
baltica
2500609751
glutamine synthetase
EC Number
Proposed Gene Annotation
Team Project Summary
Provide a 2-3 page DESCRIPTIVE SUMMARY:
(1) TEAM: Based on gene content, what parts of the pathway or cellular structure
that your team annotated appears to be functional (i.e., all components present in
P. limnophilus genome)? What components are missing from various steps or
cell structures? Propose an experiment to hunt for missing genes**. The experiment
may be computationally-based or one performed in the wet laboratory – be creative!
(No more than 5-6 sentences)
(2) INDIVIDUAL: For each assigned gene, provide a BRIEF summary of some of
the key results that enabled you to conclude that the functional annotation is
accurate as well as any interesting or surprising results that you encountered while
annotating your genes. (No more than 3-4 sentences per gene)
**NOTE: For those lab sections in which multiple teams shared one pathway or structure,
you should SHARE results – a gene isn’t missing if it was assigned to someone else.
Assemble report & turn in to your T.A.
Team BRUIN
Assigned pathway: Nitrogen Metabolism
Josie Bruin (555-555-555)
Joe Bruin (444-555-666)
Jackie Bruin (333-222-888)
Jerry Bruin (111-222-333)
Annotated Gene OIDs:
2500607069
2500609843
2500606476
2500609395
2500607068
2500607098
2500609751
2500607755
2500607482
2500606816
2500606639
2500606269
Finally, take post-annotation survey
Cookies must be enabled for survey to work properly.