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FungalG
enom
ics
and
Susta
inable
Develo
pm
ent
Gre
gButler
Depart
ment
ofCom
pute
rScie
nce
and
Software
Engin
eering
Centr
efo
rStr
uctu
raland
FunctionalG
enom
ics
Concord
iaUniv
ers
ity,
Montr
eal
www.cs.concordia.ca/~gregb
Outlin
e
Genom
ics
Enzym
es
and
Bio
-Pro
cess
ing
for
Sust
ain
able
Develo
pm
ent
Overv
iew
ofth
eFungalG
enom
ics
Pro
ject
Bio
info
rmatics
for
the
FungalG
enom
ics
Pro
ject
Conclu
sion
Bio
logy
—Tra
nscription
and
Tra
nsla
tion
Bio
logy
—Tra
nscription
Regula
tion
Bio
logy
implies
...
...
use
Multip
leSequence
Alignm
ent
(MSA)
MSA
Pro
ble
m:
Giv
en
ase
tofpro
tein
sequences,
and
an
obje
ctive
func-
tion,dete
rmin
eth
eoptim
alalignm
ent
ofth
ese
quences.
Why?
Am
ino
acid
sequence
dete
rmin
es
pro
tein
stru
ctu
re
dete
rmin
es
enzym
efu
nction
Genom
ics
and
Bio
info
rmatics
—Health
Pers
pective
Genom
ics
hig
h-t
hro
ughput,
collecting
or
using
all
genes
Genom
ics
pro
ject:
dete
rmin
efu
llchro
moso
me
sequence,pre
dic
tgenes
EST
Pro
ject:
min
em
RNA,ass
em
ble
into
”unig
enes”
Mic
roarr
ay
Pro
ject:
genom
e-o
n-a
-chip
,st
udy
gene
activity
Expre
ssio
nPro
ject:
splice
gene
into
host
,pro
duce
enzym
e
Enzym
eAss
ay
and
Chara
cte
rization
Pro
ject:
chem
istr
yand
bio
chem
istr
y
Pro
teom
ics,
...
What
isan
Enzym
e?
Enzym
eis
apro
tein
that
cata
lyse
sa
reaction.
What
isan
Enzym
e?
Enzym
es
are
very
specifi
c.
Enzym
es
are
very
effi
cie
nt
cata
lyst
s.
Industr
ialPro
cessin
gofTre
es
Industr
ialUses
ofEnzym
es:
Paper
Industr
ialUses
ofEnzym
es:
Bio
-Eth
anolfrom
Fore
str
yW
aste
Does
Bio
technolo
gy
forSusta
inability
Work
?
OECD
report
on
21
case
studie
s
wid
era
nge
of
indust
rialse
cto
rs:
pharm
aceuticals,
fine
chem
icals,
bulk
chem
icals,fo
od
and
feed,te
xtile
s,pulp
and
paper,
min
era
lsand
energ
y.
inAust
ria,Canada,G
erm
any,
Japan,th
eNeth
erlands,
the
United
Kin
g-
dom
,th
eUnited
Sta
tes
and
South
Afric
a.
“th
eir
use
invariably
leads
tore
duction
inopera
ting
cost
sorcapitalcost
sor
both
”
“New
”bio
-pro
cess
es”
can
subst
antially
reduce
em
issions
and
the
use
of
hazard
ous
raw
mate
rials.”
”T
hey
resu
ltin
fewer
by-p
roducts
,genera
tefe
wer
wast
em
ate
rials
and
consu
me
less
energ
y.”
The
Application
ofBio
technolo
gy
toIn
dust
rialSust
ain
ability,148
pages,
OECD
,Paris
2001
The
FungalGenom
ics
Pro
ject
Identify
use
fulenzym
es
for
indust
rialapplications
secre
ted
by
14
specie
soffu
ngi
by
const
ructing
cD
NA
libra
ries
with
5000
genes
per
specie
s
and
dete
cting
genes
sim
ilar
toknow
nenzym
es
and
by
const
ructing
cD
NA
mic
roarr
ay
for
each
specie
s
and
dete
cting
genes
expre
ssed
under
rela
ted
conditio
ns
Chara
cte
rize
sele
cte
denzym
es
FungalSpecie
s
Exte
rnalConte
xt
ofFungalG
enom
ics
Pro
ject
Exte
rnalConte
xt
—Public
Data
The
FungalGenom
ics
Pro
ject
What
isBio
info
rmatics?
To
store
,org
anize
&analy
ze
bio
logic
aldata
Models
—m
ath
em
atical,
statist
ical,
physical
Alg
orith
ms
—st
ring,tr
ee,gra
ph,patt
ern
s
Data
base
technolo
gy
Work
flow
and
com
puta
tionalgrids
Inte
llig
ent
reaso
nin
g—
expert
syst
em
s,agents
Web
access
,visualization,usa
bility
Rapid
syst
em
develo
pm
ent
and
evolu
tion
Bio
info
rmatics
forth
eFungalGenom
ics
Pro
ject
Aim
s
ensu
rehig
h-q
uality
experim
enta
ldata
iscollecte
d
know
quality
,confidence,pro
venance
ofdata
auto
mate
data
analy
sis
&re
port
genera
tion
Concern
s
Hid
eth
ete
chnolo
gy,
Do
the
scie
nce
Confidence
inre
sults/
inte
rpre
tation
Fle
xib
ility,
stayin
gahead
ofth
ecurv
e
Bang
for
the
buck
com
puta
tionalre
sourc
es
can
be
huge
Bio
info
rmatics
forth
eFungalGenom
ics
Pro
ject
Bio
info
rmatics
—Curr
ent
Needs
•M
ate
rials
Tra
ckin
g
•D
ata
Collection
•Q
uality
Contr
olofD
ata
and
Pro
cess
•Analy
sis
ofSequences
—Auto
mate
dAnnota
tion
•Analy
sis
ofTarg
et
Sequences
—M
anualCura
tion
•Analy
sis
ofM
icro
arr
ay
Data
—Basic
Expre
ssio
n
Bio
info
rmatics
—Futu
reNeeds
•Analy
sis
ofM
icro
arr
ay
Data
—Pro
filing
•Analy
sis
ofM
icro
arr
ay
Data
—In
tegra
ting
oth
er
Evid
ence
•Enzym
eFam
ilie
s—
Phylo
geny,
Multip
leAlignm
ent,
Cla
ssifi
ers
•Enzym
eFam
ilie
s—
Pre
dic
ting
Kin
etics
Bio
info
rmatics
Pla
tform
Bio
info
rmatics
—Housekeepin
gTasks
Mate
rials
Tra
ckin
g
identify
(bar
code
labels)
and
record
mate
rials
know
location
ofall
rele
vant
physicalm
ate
rials
know
mappin
gs
cause
dby
physicaltr
ansf
er
ofm
ate
rials
Data
Collection
keep
all
data
secure
and
access
ible
know
quality
and
pro
venance
ofall
data
support
analy
sis
and
inte
rpre
tation
ofdata
Quality
Contr
ol
know
the
quality
ofdata
pro
vid
ere
port
sto
monitor
quality
ofla
bpro
cess
es
ass
ist
india
gnosis
ofpro
ble
ms
with
lab
pro
cess
es
Bio
info
rmatics
—Analysis
Tasks
Sequence
Analysis
dete
rmin
ehig
h-q
uality
sequence
segm
ent
...
base
call
quality
,re
move
conta
min
ants
,tr
im
ass
em
ble
EST
sin
tounig
enes
Sequence
Annota
tion
sim
ilarity
again
stknow
nnucle
icand
pro
tein
sequences
...
esp
ecia
lly
again
stta
rgett
ed
enzym
efa
milie
s
searc
hfo
rpro
tein
motifs
and
dom
ain
s
isit
secre
ted
enzym
e?
oth
er
localization
info
?
cla
ssify
toG
ene
Onto
logy
cate
gory
Micro
array
Data
Analysis
norm
alize:
QC
dete
rmin
es
bad
spots
and
dynam
icra
nge
set
thre
shold
for
signifi
cant
expre
ssio
nle
vels
dete
rmin
ehig
hly
expre
ssed
genes
Conclu
sio
n
Bio
-Pro
cess
ing
using
fungalenzym
es
isa
way
tosu
stain
ability.
Bio
info
rmatics
for
findin
gand
unders
tandin
gfu
ngalenzym
es
isa
rich,
challengin
gare
afo
rin
terd
iscip
linary
rese
arc
h
Long-t
erm
Challenges
inBio
info
rmatics:
•Enzym
eFam
ily
Data
—be
able
topre
dic
tkin
etics
•Scie
ntific
Litera
ture
—be
able
tom
ine
know
ledge
•G
ene
Expre
ssio
nD
ata
—be
able
topre
dic
tfu
nction
—be
able
topre
dic
tre
gula
tion
•...
Syst
em
sBio
logy
Excitin
gtim
es
ahead
!!!
Acknowle
dgem
ents
Thank
you!
Questions?