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Oct 2, 2013 (4 years and 10 days ago)

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Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

June, 2010

Victoria

MAGPIE:
Automated Genome
Analysis and Annotation


Christoph W. Sensen


University of Calgary

Faculty of Medicine

Department of Biochemistry and Molecular Biology


csensen@ucalgary.ca

2

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

June, 2010

Victoria

Genomic Data Growth

3

Complete Genomes

According to the TIGR/NCBI listings in 2004:


176 prokaryotic genomes complete


~20 eukaryotic in some stage of assembly

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

4

MAGPIE Genome Views


June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

5

MAGPIE


Automated Genome Analysis and
Annotation


Prokaryotes, Eukaryotes, ESTs


Web
-
based Reports


Static system (most everything pre
-
computed)

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

6

MAGPIE workflow

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

7

August 26, 2009

Montreal

Clone Map

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

8

August 26, 2009

Montreal

Contig Features

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

9

August 26, 2009

Montreal

ORF Report

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

10

June, 2010

Victoria

Evidence Report

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

11

Restriction Digest

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

12

Base Composition

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

13

Repeat Analysis

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

14

tRNA Report

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

15

Metabolic Pathways

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

16

Next
-
gen EST Analysis


June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

MAGPIE overview

Histograms:

Raw 454 reads

Assembled contigs
(Paracel Transcript
Assembler or Velvet)

17

Next
-
gen EST search form with
dynamic GO help

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

18

Bluejay Browser:
later today

(Soh
et al.
, 2008)



Dynamic System


Semantically zoomable graphics


Microarray Gene Expression time series


XML
-
Java system, integrates far beyond
MAGPIE


June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

19

Linking Together View


By linking various software together we get a
new perspective and context for results

Experiment

Osprey
-
designed

microarray

Bluejay

MOBY

MAGPIE

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

20


What’s Next?


2
-
dimensional annotation will continue


3
-
dimensional annotation is emerging


Development of “cybercells”


Development of virtual organisms

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

21

Structure and Multiple
Alignment

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

22

Improving Existing Viewers


CAVE
provides wider
field of view,
more degree of
freedom for
interaction

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

23

Osteoporosis Research

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

24

Mathematical Model of Topology:

Health v. Disease

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

25

Extracting Information from the
Visual Human

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

26

Project Realism

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

27

Exploring gene expression patterns

CAVEman


Java 3D
-
based, world
-
first complete 3D human body atlas (adult male)


2,335 organs, hierarchical organization following
Terminologia

Anatomica


Numerous applications involving mapping of genetic and disease data


More information:
http://cave.ucalgary.ca/caveman

Patient MRI stack
mapped onto atlas and
registered by landmarks

Pharmacokinetics visualization

(Absorption
-
distribution
-
metabolism
-
excretion of Aspirin)

28

June, 2010

Victoria

Virtual organs: Java 3D, X3D

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

29

Highly detailed models for realistic
mapping of medical data in 3D

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

30

Working in the CAVE


June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

31

Mapping Data: Medical + Genomics

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

32

Gene Regulation in Spatial Context

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

33

Your Assignment (see binder)


Annotate each a piece of the E. coli
genome, which was analyzed and annotated
with MAGPIE


Search through assembled Poppy ESTs for
a gene of interest, view assembly,
annotated.

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform

34

MAGPIE Annotation Form

June, 2010

Victoria

Applied Computational Genomics Course

Genome Canada Integrated Bioinformatics Platform