Final Project

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Final Project

• Bioinformatics for Biologists

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Alternative B
Alternative A
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Undergraduates (Alternative A) Assigned
project Undergraduates (Alternative B) Self
designed project agreed upon in advance. Must
obtain permission from Dr. Dan Graur
Graduate Students (Alternative A) Assigned
project Graduate Students (Alternative B) Self
designed project agreed upon in advance.MUST NOT
HAVE ANYTHING TO DO WITH THE THESIS Must obtain
permission from Dr. Dan Graur
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Phylogenetic reconstructions by using
mitochondrial protein sequences (I) The
objective is to use the tools of bioinformatics
to study evolutionary relationships among taxa.
Each student will have an individual
assignment. The first part will consist of a
very short summary of the current taxonomic
knowledge pertaining to the ingroup taxa in the
assignment. This summary will be presented in
class and the PowerPoint file will be submitted
for grading.
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Phylogenetic reconstructions by using
mitochondrial protein sequences (II) In the
second part, each student will perform a
comprehensive study and submit a written report
in the form of a scientific paper.
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In the short oral presentation, the student
will 1. Describe the taxa in the assignment. 2.
Outline the current phylogenetic views pertaining
to the taxa in the assignment. 3. Describe the
methods that have been used in these studies. 4.
Present open questions (if any).
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Materials and Methods Collect all protein
sequences encoded by the mitochondria in the
ingroup. By using one ingroup sequence, identify
one or more outgroup species. Align sequences.
Construct NJ and MP trees. Bootstrap the
trees. Estimate branch lengths. Identify
groups of congruent trees.
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Based on your work 1. Does your analysis solve
the phylogenetic assignment? 2. Are there
contradicting trees? If so, what is the reason
for the incongruence? 3. Does your study agree
with previous studies? Why (or Why not)? 4. Are
there large differences in the rate of evolution
among lineages? Why?
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Submit your study as a scientific
paper Abstract Summarize briefly objectives,
hypotheses, data, methods, results, and
conclusions. Introduction State purpose, review
literature, list phylogenetic hypothesis to be
tested. Materials and Methods Provide details of
sequences and methods, present succinct
description of data collection, provide
sufficient detail to allow precise replication of
the study. Results Summarize data in tabular or
graphic form, present data without
interpretation, describe important aspects of
data. Discussion Provide interpretation of
results with regard to hypotheses, compare
results with previous studies, address
limitations and sources of errors, summarize
major conclusions. Bibliography List at least 3
literature sources.
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Bonus points Two questions related to genomics,
2D, 3D, codon usage, etc.
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Example Identify the phylogenetic relationships
within Crustacea. Your study should include 1
species belonging to the Maxillopoda, 1 species
belonging to the Pentastomida, 1 species
belonging to the Brachipoda, 1 species belonging
to the Malacostraca, 1 species belonging to the
Cephalocardia, 1 species belonging to the
Remipedia, 1 species belonging to the Ostracoda
the closest outgroup to all these taxa that you
can find.