DOTM Bioinformatics Workshop - Visual Genomics Centre

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Genome Canada

Designing oil seeds for tomorrow’s market

Project



Bioinformatics Team Progress Update

Dec
9
th
,
2008

Outline


Team collaborations


EST analysis


Software development, adoption and updates


DOTM bioinformatics workshop


DOTM bioinformatics needs survey ~ revisited


Work plan

Team Collaborations


New team personnel :


Ye Zhang

-

U of C, (COE)


Fred Peng

-

U of A


Bioinformatics team from Calgary and
Edmonton met on September
26
th
,
2008
to
review needs survey results, and planning.


Held teleconference between Calgary,
Edmonton and NRC
-
PBI on October
21
st
,
2008
to finalize planning of DOTM bioinformatics
workshop.


Provided bioinformatics support to other teams
of the project upon request

Team Collaborations Cont’d


DOTM internal project Wiki


A tool to facilitate group communication and
information exchange


Team Collaborations Cont’d


DOTM internal project Wiki


Accounts have been made for all P.I.


Currently holds information on
6
DOTM
Groups


Encourage all groups to participate and use
the wiki to share and accumulate
information.


Bioinformatics team details are available and
up
-
to
-
date to promote better transparency



EST Analysis


Obtained species information for previous
295
,
657

PBI EST sequences.


Separately ran EST assembly by species for


1
,
700

Brassica Carinata


20
,
650

Brassica Oleracea


176
,
263

Brassica Napus


22
,
651
Brassica Rapa


Submitted each species set into the
MAGPIE/Sprockets data analysis pipeline for
automated annotation and classification



Software Development, Adoption, Update


Canola tilling database:


The search function has been created to allow tilling
data search by organism and by gene names.
(Parameters can be expanded as the db becomes
more complex)


Phenomics database:


Preliminary design underway


Major data types, fields and relationships are being
identified.


Software Development and Adoption


SNP discovery pipeline


Requested for SNP
marker design


In silico detection of
putative SNPs using
project generated
EST sequences.


Web interface
developed to allow
user access to the
pipeline


Software Development and Adoption


SNP discovery pipeline


Uses existing SNP detection program:
Polybayes


Takes advantage of trace values available for
project EST sequences.

Query
Sequence
cleanup
using PTA
Scylla
executable
to identify
repeat
elements
and
contaminant
s.

Query
sequen
ce

Similar ESTs are
obtained from
BLASTn search
hits of query
against a
DOTM brassica
DB.


Set of
similar ESTs
are aligned
and a
consensus
sequence is
created
using PTA’s
modified
CAP
4

Polybayes

called to
filter
paralogs

from the
assembled
contig

and
detection of
reliable
SNPs

Result
reporting,
visualization of
sequence
tracefiles

with
BCM
traceviewer

for
validation of
SNP sites.

DOTM
Brassica

EST
databases

Consens
us
sequenc
e

Individua
l Seq.
Quality
informati
on

Cleanup

Search

Assembly

SNP
Detection

Web Interface

a priori
polymorp
hic rates

DOTM Bioinformatics Workshop


November
20
th
,
21
st
,
2008


COE, Calgary

DOTM Bioinformatics Workshop Cont’d


To introduce researchers to the various
bioinformatics tool available to them through
the DOTM portal.


To provide a forum for discussion of additional
functionality needed as well as provide
feedback on existing tools.

DOTM Bioinformatics Workshop Cont’d


Topics included


DOTM portal introduction


EST sequence processing & analysis


Microarray gene expression analysis


Oligonucleotide/Primer design


Other bioinformatics tools available at the
COE

DOTM Bioinformatics Workshop Cont’d


Feedback for providing a guideline to direct
our work on developing useful applications.


Need for EST Library information


Need for sharing/compilation of microarray data,
Tilling data


SprocketsView, Magpie minor bugs and adjustments


Detailed report in Bioinformatics section of
the DOTM wiki


DOTM Bioinformatics Needs Survey
-

Revisited


Aim:


Understand DOTM researchers’ bioinformatics needs


Participants:


All DOTM researchers (this should include PIs, RAs,
PDFs, and grad students)


Survey methods:


Online survey by using SurveyMonkey (
10
questions)


Responses:


Collected
13
responses in total


DOTM Bioinformatics Needs Survey


Response Summary


Data Type produced in the DOTM project:


Expressed sequence data (ESTs)


Tilling


Microarray


Proteomics


Markers


Large amount of phenotypic data


Metabolite profile


Field data, Seed quality data (NIRS, wet chemistry)
and QTL data

DOTM Bioinformatics Needs Survey


Response Summary (Cont’d)


How are the DOTM researchers sharing
data/information currently:


Paper based (
27
%)


Mail

(
18
%)


Email

(
100
%)


Web
-
based database sharing

(
36
%)


Conference calls and DOTM meetings

DOTM Bioinformatics Needs Survey


Response Summary (Cont’d)


The resources people want to get from the
other groups/teams:


Marker information


Mapping information


NIRS analysis of seed and NIRS calibration


Microarray data


Protocols


Experience of other researchers with
new/specialized protocols they have developed or
standardized


Trait information (yield, seed color)


Phenotypic data


Tools for various chemical analysis



DOTM Bioinformatics Needs Survey


Response Summary (Cont’d)


Use biological
information sources


(database/program to
retrieve/add
information about
biological sequences)?


Do computer
based analysis


DOTM Bioinformatics Needs Survey


Response Summary (Cont’d)


The customized bioinformatics tools DOTM
researchers want:


Primer designer




(
70
%)


Genomic annotation tool



(
60
%)


Simple sequence repeats finder


(
50
%)


cDNA library comparison


(
40
%)


Lab information management systems

(
40
%)


Marker mapping tools



(
30
%)


Microarray analysis tool



(
20
%)


“SNP finder” based on the information available
within the project


Orthologous gene finder


Gene list posting and ordering system for tilling



Bioinformatics Working Plan based on the
Survey


Make the existing tools/protocols/data
which have been requested by
researchers available through DOTM
portal
(Complete)


Developing customized tools for DOTM
researchers
(Ongoing)


Encourage people to share their data,
resource and experience within the
project
(Ongoing)


Working priorities


Plan to populate local Fiesta installation
with larger, updated EST set.


Primer design pipeline based on Osprey.


Revisit SprocketsView


Phenomic Database design


Acknowledgements


All attendees of the Bioinformatics workshop


All the researchers who participated the
survey


Paul Gordon (bioinformatician

in COE)


Erin Gilchrist in UBC


Jeff Parker