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BIOL L506 (Z620) Fall 2015

Selected Topics in Zoology (Section 15716):

BIOL L506 (Z620) Fall 2015

Course description

BIOL L506 (Z620) Bioinformatics2Go

Lecture times and locations

Tues, Thur 1:00p-2:15p, Ballentine Hall (BH) 118 (Tu), 107 (Th)

Tentative schedule (class notes can be viewed with Adobe Acrobat Reader)

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Tues Sept 29 1.1 Orientation
Introduction to WikiBCB
NCBI resources
Volker Brendel
Thur Oct 1 1.2 Molecular Phylogeny
A list of Web-servers for molecular phylogeny analyses
Mobyle @ Pasteur
BMPS Tutorial
Volker Brendel
Tues Oct 6 2.1 Genetic variation
NCBI dbSNP    How To
NCBI dbVar    How To
1000 Genomes Project    Nature 491:56
Example: rs1131769
Recent paper of interest
Volker Brendel
Thur Oct 8 2.2 Protein structure
PDB-101   - a number of wonderful tutorials!
SWISS-MODEL   - what to do if my protein is not in PDB!?
    (start here)
Volker Brendel
Tues Oct 13 3.1 Gene structure prediction
GeneSeqer (spliced alignment)
Volker Brendel
Thur Oct 15 3.2 Genome browsers and community genome annotation
yrGATE (annotation tool)
Polistes dominula xGDB instance

FlyBase (Gbrowse instance)
Volker Brendel
Tues Oct 20 4.1 Gene structure annotation: Evidence-based annotation
Volker Brendel
Thur Oct 22 1:00pm Final Projects - task and scope
The final project should be a new page in your WikiBCB name space called "final_project". The page should be a document of your learning in the class, linking the various modules in a logical fashion. The document would include an introduction that gives the relevant biological background and states a biological question you have been exploring (e.g., something about a particular gene or set of genes). You would then describe how you gathered data concerning the problem area from public databases, followed by documentation of how you used the different tools we looked at in class. Try to emphasize the logical flow going from gene to gene product; from gene to genome context; from one species to multiple species; etc. The overall goal of the final project is for you to provide a comprehensive record of your class experience in such a way that it will be a meaningful resource to you in the future. Unless you request otherwise, your WikiBCB write-ups will be made read-accessible to the world for the benefit of your fellow students, current and future, in the spirit of Wiki.
Thur Oct 22 4.2 Comparative Genomics
CoGE Workshop links
CoGE Article
Volker Brendel
Tues Oct 27 5.1 Gene expression analyses
Example: GSE29252
Motif finding in DNA and protein sequences
Volker Brendel
Thur Oct 29 5.2 Workflow design and execution tools:
BioExtract Server
Volker Brendel
Tues Nov 3 11:59pm Final Projects due students