INSTRUCTIONS This is the BIOL375 class of 2010-11. These are the students currently working with Dr. Scott on the Meiothermus ruber genome annotation project. This presentation was created by students in this course.
This is the BIOL375 class of 2010-11. These are the students currently working with Dr. Scott on the Meiothermus ruber genome annotation project. This presentation was created by students in this course.
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Mitch Anliker, Mohammed Hussain, Heather Smith, Melissa Reller, Jose Candelario Orozco
What is Meiothermus ruber?
A Genome Annotation is a process of attaching biological information to DNA sequences
Genomic Encyclopedia of Bacteria & Archaea (GEBA) is a massive JGI genome sequencing effort to fill in many of the missing or under-sampled branches of the Bacteria & Archaea trees.
*T.P. Curtis, W.T. Sloan, and J.W. Scannell. 2002. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99: 10494-10499.
First 56 GEBA genomes* filled in several missing or under-sampled branches of the Bacteria trees & showed that there is a lot of genomic diversity out there to be discovered.
* D. Wu, P. Hugenholtz, K. Mavromatis, et al., 2009. A phylogeny-driven genomic encyclopedia of Bacteria and Archaea. Nature 462: 1056-1060.
Form your argument information to DNA sequences
Large gaps in the types of bacterial genomes studied
Is there evidence to support the predictions related to my gene?
Learn the tools to analyze your gene prediction
Use the tools to collect evidence to support/refute the prediction
IMG-ACT information to DNA sequences
Most automated genome annotations - 35% are wrong
Automated annotations miss things!
Learning new and valuable information is key
Previous knowledge can help you!
Develop and strengthen genome annotation skills such as:
Using computer programs to analyze sequence data
Gathering and evaluating information from Web-based community-accessible sequence databases
Evaluating automated gene calls
Produce quality annotations for incorporation into the Integrated Microbial Genomes Database
Build conceptual understanding of:
Evolutionary relationships among genomes
Power and limitations of bioinformatics
Protein structure and function
Transcriptional and translational signals
Develop basic scientific research skills such as:
Reading and evaluating primary literature
Developing hypotheses and interpreting data
Drawing conclusions from a collection of evidence
Working with real data
Emphasizes biological root of bioinformatics
More easily compatible with education
Emphasizes complementarity of tools
Allows addition and removal of modules to match student level
Module Title information to DNA sequences
Mod 1: Basic Information
DNA coordinates & base sequence, amino acid sequence, pI
Mod 2: Sequence-based Similarity Data
Sequence alignment, conserved protein domains and protein families
Mod 3: Cellular Localization Data
Signal peptide sequence, transmembrane domains
The future is now!!! information to DNA sequences