Data integration and analyses:

1
Data integration and analyses a challenge for
culture collections Vincent Robert Centraalbure
au voor Schimmelcultures, Utrecht, The
Netherlands
2
Outline

• The problem of dispersed data
• The diversity of data
• The need for non-static databases
• Algorithms problems
• BioloMICS Software
• CBS databases and MycoBank

3
1. The problem of dispersed data

• Books, papers
• The Yeasts, a taxonomic study, 4th
  Kurtzman,C.P.,Fell,J.W. ed., Amsterdam Elseviers
  Scientific.
• Yeasts Characteristics and Identification. Third
  Edition. Barnett,J.A.,Payne,R.W.,Yarrow,D.
  Cambridge Cambridge University Press.
• IJSEM
• Antonie van Leeuwenhoek
• FEMS Yeast Research

4
1.The problem of dispersed data

• Books, papers
• The Yeasts, a taxonomic study, 4th
  Kurtzman,C.P.,Fell,J.W. ed., Amsterdam Elseviers
  Scientific.
• Yeasts Characteristics and Identification. Third
  Edition. Barnett,J.A.,Payne,R.W.,Yarrow,D.
  Cambridge Cambridge University Press.
• IJSEM
• Antonie van Leeuwenhoek
• FEMS Yeast Research
• Internet
• CBS yeast database at www.cbs.knaw.nl/yeast.htm
• www.yeastgenome.org/VL-yeast.html
• Yeast Proteome Database (YPD)
• GenBank

5
1. The problem of dispersed data

• Books, papers
• The Yeasts, a taxonomic study, 4th
  Kurtzman,C.P.,Fell,J.W. ed., Amsterdam Elseviers
  Scientific.
• Yeasts Characteristics and Identification. Third
  Edition. Barnett,J.A.,Payne,R.W.,Yarrow,D.
  Cambridge Cambridge University Press.
• IJSEM
• Antonie van Leeuwenhoek
• FEMS Yeast Research
• Internet
• CBS yeast database at www.cbs.knaw.nl/yeast.htm
• www.yeastgenome.org/VL-yeast.html
• Yeast Proteome Database (YPD)
• GenBank
• Catalogs
• ATCC, CBS, DBVPG, DSM, IFO, JCM, MUCL, NCYC,
  NITE, NRRL,

6
2. The diversity of data
7
2. The diversity of data

• Taxonomically relevant data
• Nomenclature
• Bibliography
• Morphology
• Physiology
• 26S, ITS,

8
2. The diversity of data

• Taxonomically relevant data
• Nomenclature
• Bibliography
• Morphology
• Physiology
• 26S, ITS,
• Ecology
• Temperatures (min, max, averages, )
• Precipitations
• Land cover
• Elevation

9
2. The diversity of data

• Taxonomically relevant data
• Nomenclature
• Bibliography
• Morphology
• Physiology
• 26S, ITS,
• Ecology
• Temperatures (min, max, averages, )
• Precipitations
• Land cover
• Elevation
• Industrially useful data
• Water activity
• Optimal temperatures for growth
• Fermentation ability

10
2. The diversity of data

• Taxonomically relevant data
• Nomenclature
• Bibliography
• Morphology
• Physiology
• 26S, ITS,
• Ecology
• Temperatures (min, max, averages, )
• Precipitations
• Land cover
• Elevation
• Industrially useful data
• Water activity
• Optimal temperatures for growth
• Fermentation ability
• Medically important information

11
3. The need for non-static databases

• Simple searching

12
3. The need for non-static databases

• Simple searching
• IDs using polyphasic approaches

13
3. The need for non-static databases

• Simple searching
• IDs using polyphasic approaches
• Types and amount of data are changing all the
  time morphology gt physiology gt gels gt DNA gt
  proteins

14
3. The need for non-static databases

• Simple searching
• IDs using polyphasic approaches
• Types and amount of data are changing all the
  time morphology gt physiology gt gels gt DNA gt
  proteins
• DNA chips capable databases

15
4. Algorithms problems
16
4. Algorithms problemsExample 1
gi2062240gbU45755.1CLU45755 Candida
lodderae 26S riboso... 492 e-136
gi2062200gbU45799.1CAU45799 Candida
atlantica 26S ribos... 492 e-136
gi1172134gbU43387.1EAU43387 Eremothecium
ashbyi 26S rib... 492 e-136
gi11527568dbjAB034689.1AB034689 Candida
tropicalis gene... 492 e-136
gi8099636gbAF257268.1AF257268 Candida
tropicalis KCTC 7... 490 e-136
gi10717179gbAY007890.1 Saccharomyces
dairenensis 26S ri... 490 e-136
gi4038913gbU84228.1HOU84228 Hanseniaspora
osmophila 26S... 490 e-136 gi4038756gbU695
77.1KWU69577 Kluyveromyces wickerhamii 2...
490 e-136 gi4038752gbU69575.1KDU69575
Kluyveromyces dobzhanskii 2... 490 e-136
gi4038749gbU69579.1KAU69579 Kluyveromyces
aestuarii 26S... 490 e-136 gi2062249gbU457
59.1CNU45759 Candida naeodendra 26S ribo...
490 e-136 gi2062237gbU45791.1CIU45791
Candida insectorum 26S ribo... 490 e-136
gi2062220gbU45750.1CDU45750 Candida
diddensiae 26S ribo... 490 e-136
gi2065487gbU45849.1CGU45849 Candida
glucosophila 26S ri... 490 e-136
gi16755506gbAF335974.1AF335974 Pichia
farinosa strain C... 488 e-135
gi12751165gbAF313365.1AF313365
Sporopachydermia sp. UWO... 488 e-135
gi4090564gbU76532.1SQU76532
Sporopachydermia quercuum 2... 488 e-135
gi4038836gbU74590.1PCU74590 Pichia
chambardii 26S large... 488 e-135
gi4038741gbU68556.1SDU68556 Saccharomyces
dairensis 26S... 488 e-135 gi2062301gbU457
39.1PFU45739 Pichia farinosa 26S ribosom...
488 e-135 gi2062213gbU45744.1CCU45744
Candida cacaoi 26S ribosoma... 488 e-135
gi2062310gbU45765.1PPU45765 Pichia
philogaea 26S riboso... 486 e-134
gi16755503gbAF335971.1AF335971 Pichia
fabianii strain U... 484 e-134
gi4038982gbAF017241.1AF017241 Candida
mycetangii 26S la... 484 e-134
gi4038916gbU84226.1KLU84226 Kloeckera
lindneri 26S ribo... 484 e-134
gi4038825gbU73576.1PVU73576 Pichia veronae
26S ribosoma... 484 e-134 gi4038822gbU7357
3.1PFU73573 Pichia fabianii 26S ribosom...
484 e-134 gi4038813gbU73596.1HVU73596
Hanseniaspora valbyensis 26... 484 e-134
gi4038761gbU69877.1CMU69877 Candida
maritima 26S riboso... 484 e-134
gi4038757gbU69582.1KWU69582 Kluyveromyces
waltii 26S ri... 482 e-133 gi16755505gbAF3
35973.1AF335973 Pichia farinosa strain U...
480 e-133 gi14150783gbAF374610.1AF374610
Candida zeylanoides 26S ... 478 e-132
gi4038910gbU76204.1CLU76204 Candida
lyxosophila 26S rib... 478 e-132
gi4038834gbU74589.1PBU74589 Pichia bispora
26S large su... 478 e-132 gi2062242gbU4580
1.1CLU45801 Candida lyxosophila 26S rib...
478 e-132 gi4038914gbU84229.1HUU84229
Hanseniaspora uvarum 26S ri... 476 e-131
gi4038911gbU84230.1HGU84230 Hanseniaspora
guilliermondi... 476 e-131 gi2065495gbU458
35.1CVU45835 Candida valdiviana 26S ribo...
476 e-131 gi16755510gbAF335978.1AF335978
Kluyveromyces marxianus ... 474 e-131
gi6683907gbAF202901.1AF202901
Sporopachydermia sp. D76-... 474 e-131
gi4038945gbU94924.1KMU94924 Kluyveromyces
marxianus 26S... 474 e-131 gi4038943gbU949
22.1KLU94922 Kluyveromyces lactis 26S ri...
474 e-131 gi4038940gbU94919.1KLU94919
Kluyveromyces lactis 26S ri... 474 e-131
gi4038912gbU84225.1HOU84225 Hanseniaspora
occidentalis ... 474 e-131 gi14581411gbAY0
13719.1 Candida xylopsoci 26S ribosomal ...
472 e-130 gi4038990gbAF017249.1AF017249
Candida ulmi 26S large su... 472 e-130
gi4038772gbU70184.1CQU70184 Candida
quercuum 26S riboso... 472 e-130
gi2655937embY15471.1CZY15471 Candida
zeylanoides 25S rR... 472 e-130
gi2655933embY15467.1CGY15467 Candida
glabrata 25S rRNA ... 472 e-130
gi6502550gbAF113137.1AF113137 Eremothecium
gossypii 5S ... 470 e-130 gi8099641gbAF257
273.1AF257273 Hanseniaspora uvarum KCTC...
470 e-130 gi8575727gbAF267497.1AF267497
Candida tropicalis 26S ri... 470 e-130
gi2062337gbU57685.1CDU57685 Candida
dubliniensis 26S ri... 470 e-130
gi1172136gbU43389.1EGU43389 Eremothecium
gossypii 26S r... 470 e-130
gi14150782gbAF374609.1AF374609 Candida
parapsilosis 26S... 468 e-129
gi2062199gbU45779.1CAU45779 Candida
atmosphaerica 26S r... 468 e-129
gi8925824gbAF153674.1AF153674 Pichia
ramenticola 26S ri... 466 e-128
gi4038986gbAF017245.1AF017245 Pichia
ramenticola 26S la... 466 e-128
gi4038918gbU84232.1SRU84232 Saccharomyces
rosinii 26S r... 466 e-128 gi12751167gbAF3
13367.1AF313367 Kluyveromyces cf. yarrow...
464 e-128 gi4038904gbU76198.1AHU76198
Ascoidea hylecoeti 26S ribo... 464 e-128
gi2655938embY15472.1CBY15472 Candida
boleticola 25S rRN... 464 e-128
gi15077519gbAF339904.1AF339904
Zygosaccharomyces kombuc... 462 e-127
gi5732687gbAF156538.1AF156538 Candida
albicans strain A... 462 e-127
gi5732686gbAF156537.1AF156537 Candida
albicans strain T... 462 e-127
gi5732685gbAF156536.1AF156536 Candida
albicans strain A... 462 e-127
gi9454235gbAF272396.1AF272396 Candida sp.
HA1034 26S ri... 462 e-127 gi4039012gbAF01
7728.1 Zygosaccharomyces sp. NRRL YB-481...
462 e-127 gi2062198gbU45776.1CAU45776
Candida albicans 26S riboso... 462 e-127
gi454300gbL28817.1YSARRB Candida albicans
internal tran... 462 e-127 gi6635244dbjAB0
31020.1AB031020 Candida dubliniensis gen...
462 e-127 gi14581406gbAY013714.1 Candida
prunicola 26S ribosomal ... 460 e-127
gi695505embZ48568.1CNRRNAV3 C.norvegensis
gene for larg... 460 e-127 gi4038745gbU685
55.1SPU68555 Saccharomyces paradoxus 26S...
458 e-126 gi2655941embY15475.1CPY15475
Candida populi 25S rRNA ge... 458 e-126
gi4038833gbU74596.1PAU74596 Pichia alni 26S
large subun... 456 e-125 gi4038787gbU70251
.1CBU70251 Candida boidinii 26S ribosa... 456
e-125 gi1172135gbU43388.1ECU43388
Eremothecium cymbalariae 26... 456 e-125
gi14150787gbAF374614.1AF374614
Kluyveromyces lactis 26S... 454 e-125
gi671812embX70659.1CA25S C.albicans 25S
rRNA 454 e-125
gi14581407gbAY013715.1 Candida pyralidae
26S ribosomal ... 452 e-124
gi2443760gbAF020437.1AF020437 Pichia
fermentans 26S rib... 452 e-124
gi10717184gbAY007895.1 Saccharomyces sp.
CBS6904 26S ri... 450 e-124
gi15637396gbAF406921.1AF406921
Saccharomyces servazzii ... 450 e-124
gi10717209gbAY007920.1 Saccharomyces
unisporus strain C... 450 e-124
gi10717208gbAY007919.1 Saccharomyces
unisporus strain C... 450 e-124
gi10717207gbAY007918.1 Saccharomyces
unisporus strain C... 450 e-124
gi10717206gbAY007917.1 Saccharomyces
unisporus strain C... 450 e-124
gi10717205gbAY007916.1 Saccharomyces
unisporus strain C... 450 e-124
gi10717204gbAY007915.1 Saccharomyces
unisporus strain C... 450 e-124
gi10717203gbAY007914.1 Saccharomyces
unisporus strain C... 450 e-124
gi10717202gbAY007913.1 Saccharomyces
unisporus strain C... 450 e-124
gi10717201gbAY007912.1 Saccharomyces
unisporus strain N... 450 e-124
gi4090565gbU76531.1SSU76531 Stephanoascus
smithiae 26S ... 450 e-124 gi4038809gbU721
63.1ZRU72163 Zygosaccharomyces rouxii 26...
450 e-124 gi4038808gbU72162.1ZBU72162
Zygosaccharomyces bisporus ... 450 e-124
gi4038781gbU70245.1CEU70245 Candida edax
26S ribosomal ... 450 e-124
gi4038748gbU68554.1SUU68554 Saccharomyces
unisporus 26S... 450 e-124 gi4038746gbU685
58.1SSU68558 Saccharomyces servazzii 26S...
450 e-124 gi4038737gbU68551.1KLU68551
Kluyveromyces lodderae 26S ... 450 e-124
gi2065512gbU45851.1SLU45851
Sporopachydermia lactativor... 450 e-124
gi2655936embY15470.1CBY15470 Candida bombi
25S rRNA gen... 450 e-124 gi4090561gbU7652
9.1SCU76529 Sporopachydermia cereana 26...
448 e-123 gi4038977gbAF017236.1 Candida
bertae var. chiloensis 26... 448 e-123
gi4038967gbU94946.1SSU94946 Saccharomycodes
sinensis 26... 448 e-123 gi4038963gbU94942
.1NFU94942 Nadsonia fulvescens var. el... 448
e-123 gi2065509gbU45825.1NFU45825
Nadsonia fulvescens 26S rib... 448 e-123
gi1072140gbU40089.1SSU40089
Schizoblastosporion starkey... 448 e-123
gi2065494gbU45833.1CVU45833 Candida vinaria
26S ribosom... 446 e-122 gi13488599gbAY028
434.1 Candida suzukii 26S ribosomal RN... 444
e-122 gi4038936gbU84346.1KPU84346
Kluyveromyces piceae 26S ri... 442 e-121
gi4038751gbU69583.1KBU69583 Kluyveromyces
bacillisporus... 442 e-121 gi4100446gbAF00
5703.1AF005703 Saccharomyces paradoxus 2...
438 e-120 gi2062278gbU45816.1CTU45816
Candida tepae 26S ribosomal... 438 e-120
gi2062238gbU45718.1CKU45718 Candida kruisii
26S ribosom... 438 e-120 gi2062216gbU45807
.1CCU45807 Candida castrensis 26S ribo... 438
e-120 gi2062211gbU45806.1CBU45806 Candida
bondarzewiae 26S ri... 438 e-120
gi2062203gbU45812.1CAU45812 Candida
antillancae 26S rib... 438 e-120
gi2065491gbU45826.1CPU45826 Candida
paludigena 26S ribo... 438 e-120
Score E Sequences producing significant
alignments (bits)
Value gi4038947gbU94926.1COU94926 Candida
ooitensis 26S ribos... 1116 0.0
gi8895067gbAF153672.1AF153672 Candida
piceae 26S riboso... 797 0.0
gi4038900gbU75966.1WSU75966 Williopsis
salicorniae 26S ... 797 0.0
gi4038774gbU70185.1CSU70185 Candida
sonorensis 26S ribo... 787 0.0
gi4038875gbU75723.1PTU75723 Pichia
trehalophila 26S rib... 781 0.0
gi13876581gbAY029357.1 Pichia pilisensis
strain NCAIM Y... 773 0.0
gi12964776gbAF322056.1AF322056 Candida sp.
UWO(PS)00-14... 761 0.0 gi4038864gbU7551
5.1PMU75515 Pichia minuta 26S ribosomal...
755 0.0 gi4038788gbU70252.1CPU70252
Candida pini 26S ribosomal ... 755 0.0
gi4038866gbU75523.1PMU75523 Pichia
methanolica 26S ribo... 751 0.0
gi14582588gbAF283568.1AF283568 Candida sp.
SKB2 26S rib... 741 0.0 gi4038865gbU7551
8.1PMU75518 Pichia minuta 26S ribosomal...
741 0.0 gi4038989gbAF017248.1AF017248
Candida arabinofermentans... 737 0.0
gi15341456gbAF403148.1AF403148 Pichia
salicis 26S ribos... 733 0.0
gi4038860gbU75517.1PFU75517 Pichia
finlandica 26S ribos... 733 0.0
gi4038771gbU70183.1CPU70183 Candida
pignaliae 26S ribos... 731 0.0
gi15341454gbAF403146.1AF403146 Pichia
dorogensis 26S ri... 726 0.0
gi4038858gbU75524.1PAU75524 Pichia angusta
26S ribosoma... 716 0.0 gi15341455gbAF40
3147.1AF403147 Pichia zsoltii 26S ribos...
710 0.0 gi4038784gbU70248.1COU70248
Candida ovalis 26S ribosoma... 710 0.0
gi4038782gbU70246.1CNU70246 Candida
nemodendra 26S ribo... 708 0.0
gi15341453gbAF403145.1AF403145 Pichia
trehaloabstinens ... 700 0.0
gi12751150gbAF313350.1AF313350 Candida
ortonii large su... 698 0.0
gi4038861gbU75520.1PGU75520 Pichia
glucozyma 26S riboso... 692 0.0
gi4038863gbU75525.1PKU75525 Pichia kodamae
26S ribosoma... 684 0.0 gi20067079gbAF49
0419.1 Candida sonorensis DBVPG 7193 26...
682 0.0 gi4038862gbU75519.1PHU75519
Pichia henricii 26S ribosom... 678 0.0
gi20067078gbAF490418.1 Candida sonorensis
DBVPG 7192 26... 674 0.0 gi13876580gbAY0
29356.1 Candida hungarica strain NCAIM Y...
670 0.0 gi13876579gbAY029355.1 Candida
hungarica strain NCAIM Y... 670 0.0
gi4038869gbU75527.1PPU75527 Pichia pinus
26S ribosomal ... 670 0.0
gi20067080gbAF490420.1 Candida sonorensis
DBVPG 7194 26... 668 0.0 gi20067081gbAF4
90421.1 Candida sonorensis DBVPG 7198 26...
666 0.0 gi20067075gbAF490415.1 Candida
sonorensis DBVPG 7183 26... 666 0.0
gi20067074gbAF490414.1 Candida sonorensis
DBVPG 7180 26... 666 0.0 gi20067072gbAF4
90412.1 Candida sonorensis DBVPG 7175 26...
666 0.0 gi4038767gbU70186.1CMU70186
Candida methanosorbosa 26S ... 666 0.0
gi4038768gbU70180.1CNU70180 Candida
nitratophila 26S ri... 662 0.0
gi4038766gbU70181.1CMU70181 Candida maris
26S ribosomal... 662 0.0 gi1100959gbU401
28.1ACU40128 Ambrosiozyma cicatricosa 26...
660 0.0 gi20067076gbAF490416.1 Candida
sonorensis DBVPG 7186 26... 658 0.0
gi4038857gbU75521.1PAU75521 Pichia
angophorae 26S ribos... 654 0.0
gi1100929gbU40106.1AMU40106 Ambrosiozyma
monospora 26S ... 654 0.0
gi20067073gbAF490413.1 Candida sonorensis
DBVPG 7177 26... 652 0.0 gi4038818gbU736
05.1AAU73605 Ambrosiozyma ambrosiae 26S ...
652 0.0 gi20067071gbAF490411.1 Candida
sonorensis DBVPG 7172 26... 650 0.0
gi4038764gbU70188.1CCU70188 Candida
cariosilignicola 26... 650 0.0
gi1100930gbU40113.1APU40113 Ambrosiozyma
philentoma 26S... 646 0.0
gi2655934embY15468.1CBY15468 Candida
boidinii 25S rRNA ... 644 0.0
gi1072125gbU40083.1APU40083 Ambrosiozyma
platypodis 26S... 636 e-180
gi4038867gbU75526.1PMU75526 Pichia
methylivora 26S ribo... 634 e-179
gi20067077gbAF490417.1 Candida sonorensis
DBVPG 7188 26... 622 e-176 gi4038873gbU757
24.1PNU75724 Pichia naganishii 26S ribos...
618 e-174 gi12382229gbAF245400.1AF245400
Candida pomiphila 26S ri... 605 e-170
gi4038765gbU70190.1CLU70190 Candida
llanquihuensis 26S ... 605 e-170
gi13488598gbAY028433.1 Candida sp. NCAIM
1162 26S ribos... 603 e-170
gi12382231gbAF245402.1AF245402 Candida
cidri 26S riboso... 603 e-170
gi4038859gbU75516.1PCU75516 Pichia
capsulata 26S riboso... 601 e-169
gi4038868gbU75522.1PPU75522 Pichia
philodendra 26S ribo... 595 e-167
gi4038949gbU94928.1CCU94928 Candida
cellulolytica 26S r... 591 e-166
gi4038946gbU94925.1CMU94925 Candida
methanolophaga 26S ... 591 e-166
gi4038775gbU70189.1CSU70189 Candida
succiphila 26S ribo... 591 e-166
gi2065492gbU45831.1CQU45831 Candida
quercitrusa 26S rib... 591 e-166
gi12751166gbAF313366.1AF313366 Candida cf.
nanaspora UW... 589 e-165 gi12382232gbAF24
5403.1AF245403 Candida anglica 26S ribo...
583 e-164 gi2062250gbU45818.1CNU45818
Candida natalensis 26S ribo... 583 e-164
gi2062218gbU45821.1CCU45821 Candida
chilensis 26S ribos... 583 e-164
gi8895068gbAF153673.1AF153673 Candida
wyomingensis 26S ... 581 e-163
gi4038779gbU70243.1CWU70243 Candida
wickerhamii 26S rib... 581 e-163
gi4038776gbU70178.1PCU70178 Pichia
capsulata 26S riboso... 577 e-162
gi2062246gbU45782.1CMU45782 Candida
multigemmis 26S rib... 575 e-161
gi4038796gbU71066.1CPU71066 Candida peltata
26S ribosom... 573 e-161 gi4038876gbU75718
.1PXU75718 Pichia xylosa 26S ribosomal... 571
e-160 gi4038874gbU75720.1PTU75720 Pichia
toletana 26S ribosom... 571 e-160
gi2062253gbU45758.1CPU45758 Candida
palmioleophila 26S ... 571 e-160
gi2062228gbU45717.1CFU45717 Candida
fluviatilis 26S rib... 571 e-160
gi4038948gbU94927.1DHU94927 Debaryomyces
hansenii var. ... 567 e-159
gi2065499gbU45838.1DMU45838 Debaryomyces
marama 26S rib... 567 e-159
gi2065498gbU45846.1DCU45846 Debaryomyces
coudertii 26S ... 567 e-159
gi4038794gbU71067.1CIU71067 Candida
ishiwadae 26S ribos... 565 e-158
gi2062287gbU45808.1DHU45808 Debaryomyces
hansenii 26S r... 565 e-158
gi7649273gbAF251552.1AF251552 Candida
cleridarum large ... 563 e-158
gi14150789gbAF374616.1AF374616 Pichia
guilliermondii 26... 563 e-158
gi4038851gbU75418.1PPU75418 Pichia pijperi
26S ribosoma... 563 e-158 gi2062313gbU4576
4.1PSU45764 Pichia spartinae 26S riboso...
563 e-158 gi2062302gbU45709.1PGU45709
Pichia guilliermondii 26S r... 563 e-158
gi8099638gbAF257270.1AF257270 Pichia
guilliermondii KCT... 559 e-156
gi2062290gbU45805.1DRU45805 Debaryomyces
robertsiae 26S... 559 e-156
gi2065510gbU45848.1PIU45848 Pichia
inositovora 26S ribo... 559 e-156
gi2065506gbU45843.1DVU45843 Debaryomyces
vanrijiae var.... 559 e-156
gi2065504gbU45844.1DUU45844 Debaryomyces
udenii 26S rib... 559 e-156
gi2065500gbU45839.1DNU45839 Debaryomyces
nepalensis 26S... 559 e-156
gi2065497gbU45841.1DCU45841 Debaryomyces
castellii 26S ... 559 e-156
gi18147574dbjAB054994.1AB054994
Debaryomyces polymorphu... 559 e-156
gi18147573dbjAB054993.1AB054993
Debaryomyces prosopidis... 559 e-156
gi2062286gbU45809.1DEU45809 Debaryomyces
etchellsii 26S... 557 e-156
gi12964777gbAF322057.1AF322057 Candida sp.
UWO(PS)00-16... 555 e-155 gi12025075gbAF27
9392.1AF279392 Ambrosiozyma platypodis ...
555 e-155 gi2062344gbU62311.1CFU62311
Candida fukuyamaensis 26S r... 555 e-155
gi2062283gbU45707.1CXU45707 Candida
xestobii 26S riboso... 555 e-155
gi11345036gbAF178052.1AF178052 Candida
oleophila strain... 551 e-154
gi11345034gbAF178050.1AF178050 Candida
oleophila strain... 551 e-154
gi11345031gbAF178047.1AF178047 Candida
oleophila strain... 551 e-154
gi2062270gbU45795.1CSU45795 Candida
schatavii 26S ribos... 551 e-154
gi2062269gbU45794.1CSU45794 Candida
santamariae var. sa... 551 e-154
gi2062259gbU45800.1CRU45800 Candida
railenensis 26S rib... 551 e-154
gi2062251gbU45793.1COU45793 Candida
oleophila 26S ribos... 551 e-154
gi2062210gbU45798.1CBU45798 Candida beechii
26S ribosom... 551 e-154 gi1072127gbU40091
.1CFU40091 Cephaloascus fragrans 26S r... 551
e-154 gi2065507gbU45837.1DYU45837
Debaryomyces yamadae 26S ri... 551 e-154
gi2065505gbU45842.1DVU45842 Debaryomyces
vanrijiae var.... 551 e-154
gi2065502gbU45836.1DPU45836 Debaryomyces
polymorphus 26... 551 e-154
gi4038785gbU70249.1CPU70249 Candida populi
26S ribosoma... 549 e-153 gi4038780gbU7024
4.1CAU70244 Candida anatomiae 26S ribos...
549 e-153 gi17979027gbAY069955.1 Candida
flocculosa strain NCAIM ... 547 e-153
gi8099642gbAF257274.1AF257274 Candida
railenensis KCTC ... x
gi4038773gbU70179.1CSU70179 Candida solani
26S ribosoma... 547 e-153 gi2062268gbU4578
5.1CSU45785 Candida santamariae var. me...
545 e-152 gi14585977gbAY040651.1 Candida
psychrophila 26S ribosom... 543 e-152
gi13236250gbAF318252.1AF318252 Uncultured
ascomycote Ma... 543 e-152 gi11345030gbAF1
78046.1AF178046 Candida oleophila strain...
543 e-152 gi2062258gbU45786.1CRU45786
Candida ralunensis 26S ribo... 543 e-152
gi2062254gbU45813.1CPU45813 Candida
psychrophila 26S ri... 543 e-152
gi2062241gbU45787.1CLU45787 Candida
laureliae 26S ribos... 543 e-152
gi2062207gbU45777.1CBU45777 Candida
boleticola 26S ribo... 543 e-152
gi2065503gbU45845.1DPU45845 Debaryomyces
pseudopolymorp... 543 e-152
gi1072107gbU39474.1CAU39474 Cephaloascus
albidus 26S ri... 543 e-152
gi4038942gbU94921.1CKU94921 Candida
karawaiewii 26S rib... 541 e-151
gi4038777gbU70241.1CEU70241 Candida ernobii
26S ribosom... 541 e-151 gi4038872gbU75722
.1PHU75722 Pichia holstii 26S ribosoma... 539
e-150 gi4038797gbU71072.1CPU71072 Candida
pseudoglaebosa 26S ... 539 e-150
gi4038792gbU71071.1CFU71071 Candida fragi
26S ribosomal... 539 e-150 gi2062311gbU457
41.1PSU45741 Pichia stipitis 26S ribosom...
539 e-150 gi2062267gbU45773.1CSU45773
Candida shehatae var. insec... 539 e-150
gi2062266gbU45772.1CSU45772 Candida
shehatae var. ligno... 539 e-150
gi2062264gbU45761.1CSU45761 Candida
shehatae var. sheha... 539 e-150
gi2062232gbU45757.1CGU45757 Candida
glaebosa 26S riboso... 539 e-150
gi2062312gbU45742.1PSU45742 Pichia
segobiensis 26S ribo... 537 e-150
gi2062285gbU45743.1DCU45743 Debaryomyces
carsonii 26S r... 537 e-150
gi2062208gbU45778.1CBU45778 Candida
buinensis 26S ribos... 537 e-150
gi11345033gbAF178049.1AF178049 Candida
oleophila strain... 535 e-149
gi11345032gbAF178048.1AF178048 Candida
oleophila strain... 535 e-149
gi2062317gbU45719.1WFU45719 Wickerhamia
fluorescens 26S... 535 e-149
gi2065496gbU45832.1CZU45832 Candida
zeylanoides 26S rib... 535 e-149
gi2065489gbU45853.1CKU45853 Candida krissii
26S ribosom... 535 e-149 gi4038843gbU74594
.1PSU74594 Pichia sydowiorum 26S large... 531
e-148 gi4038837gbU74598.1PHU74598 Pichia
hampshirensis 26S la... 531 e-148
gi2062265gbU45762.1CSU45762 Candida
saitoana 26S riboso... 531 e-148
gi2062306gbU45797.1PMU45797 Pichia mexicana
26S ribosom... 529 e-147 gi2062281gbU45783
.1CVU45783 Candida veronae 26S ribosom... 529
e-147 gi2062277gbU45784.1CTU45784 Candida
terebra 26S ribosom... 529 e-147
gi2062247gbU45792.1CMU45792 Candida
membranifaciens 26S... 529 e-147
gi2062225gbU45790.1CEU45790 Candida
entomaea 26S riboso... 529 e-147
gi18483225gbAF466178.1 Pichia dianae 26S
ribosomal RNA ... 527 e-147
gi4038770gbU70182.1COU70182 Candida
odintsovae 26S ribo... 527 e-147
gi2065501gbU45840.1DOU45840 Debaryomyces
occidentalis v... 527 e-147
gi4038950gbU94929.1WSU94929 Williopsis
saturnus var. mr... 523 e-146
gi4038899gbU75960.1WSU75960 Williopsis
saturnus var. su... 523 e-146
gi4038891gbU75959.1CMU75959 Citeromyces
matritensis 26S... 523 e-146
gi4038841gbU74591.1PSU74591 Pichia
strasburgensis 26S l... 523 e-146
gi4038828gbU73579.1PJU73579 Pichia japonica
26S ribosom... 523 e-146 gi2062214gbU45747
.1CCU45747 Candida coipomoensis 26S ri... 523
e-146 gi4038981gbAF017240.1AF017240
Candida trypodendroni 26S... 521 e-145
gi4038984gbAF017243.1AF017243 Candida
tammaniensis 26S ... 521 e-145
gi2062289gbU45804.1DOU45804 Debaryomyces
occidentalis v... 521 e-145
gi12006161gbAF271084.1AF271084 Candida
peoriaensis 26S ... 519 e-145
gi4038854gbU75423.1PRU75423 Pichia
rabaulensis 26S ribo... 519 e-145
gi2062230gbU45781.1CFU45781 Candida
friedrichii 26S rib... 519 e-145
gi2062245gbU45745.1CMU45745 Candida maltosa
26S ribosom... 517 e-144 gi11527567dbjAB03
4688.1AB034688 Candida maltosa gene fo... 517
e-144 gi11527566dbjAB034687.1AB034687
Candida maltosa gene fo... 517 e-144
gi11527565dbjAB034686.1AB034686 Candida
maltosa gene fo... 517 e-144
gi11527564dbjAB034685.1AB034685 Candida
maltosa gene fo... 517 e-144
gi18698532gbAF459657.1 Williopsis saturnus
KCTC 17042 2... 515 e-143 gi12964778gbAF32
2058.1AF322058 Candida sp. UWO(PS)00-21...
515 e-143 gi15429071gbAF330115.1AF330115
Pichia anomala strain VK... 515 e-143
gi15429070gbAF330114.1AF330114 Pichia
anomala strain CB... 515 e-143
gi15429069gbAF330113.1AF330113 Pichia
anomala strain CB... 515 e-143
gi15429068gbAF330112.1AF330112 Pichia
anomala strain CB... 515 e-143
gi15429067gbAF330111.1AF330111 Pichia
anomala strain CB... 515 e-143
gi12642545gbAF286599.1AF286599 Pichia
anomala 26S large... 515 e-143
gi4038957gbU94936.1WSU94936 Williopsis
saturnus var. sa... 515 e-143
gi4038951gbU94930.1WSU94930 Williopsis
saturnus var. su... 515 e-143
gi4038898gbU75958.1WSU75958 Williopsis
saturnus var. sa... 515 e-143
gi4038842gbU74593.1PSU74593 Pichia
subpelliculosa 26S l... 515 e-143
gi4038835gbU74587.1PCU74587 Pichia ciferrii
26S large s... 515 e-143 gi4038832gbU74592
.1PAU74592 Pichia anomala 26S large su... 515
e-143 gi4038827gbU73578.1PMU73578 Pichia
meyerae 26S ribosoma... 515 e-143
gi4038763gbU69875.1CVU69875 Candida
vartiovaarae 26S ri... 515 e-143
gi2062282gbU45775.1CSU45775 Candida sp. 26S
ribosomal R... 515 e-143 gi2062252gbU45754
.1CPU45754 Candida parapsilosis 26S ri... 515
e-143 gi4038928gbU84236.1ZCU84236
Zygosaccharomyces cidri 26S... 513 e-143
gi2062315gbU45796.1PTU45796 Pichia
triangularis 26S rib... 513 e-143
gi2062292gbU45763.1LEU45763 Lodderomyces
elongisporus 2... 513 e-143
gi2062215gbU45789.1CCU45789 Candida
conglobata 26S ribo... 513 e-143
gi2062209gbU45780.1CBU45780 Candida butyri
26S ribosoma... 513 e-143 gi2062201gbU4580
2.1CAU45802 Candida aaseri 26S ribosoma...
513 e-143 gi2062224gbU45746.1CEU45746
Candida ergastensis 26S rib... 511 e-142
gi2065486gbU45823.1CCU45823 Candida
cylindracea 26S rib... 509 e-142
gi4039003gbAF017408.1AF017408 Pichia sp.
NRRL Y-7615 26... 507 e-141
gi4038839gbU74597.1PMU74597 Pichia
mississippiensis 26S... 507 e-141
gi4038838gbU74595.1PLU74595 Pichia
lynferdii 26S large ... 507 e-141
gi4038826gbU73577.1PAU73577 Pichia
amylophila 26S ribos... 507 e-141
gi4038823gbU73574.1PBU73574 Pichia
bimundalis 26S ribos... 507 e-141
gi4038821gbU73572.1PPU73572 Pichia
petersonii 26S ribos... 507 e-141
gi6683926gbAF202920.1AF202920
Sporopachydermia sp. 94-2... 505 e-140
gi4038929gbU84239.1ZFU84239
Zygosaccharomyces fermentat... 505 e-140
gi4038824gbU73575.1PAU73575 Pichia
americana 26S riboso... 505 e-140
gi4038817gbU73604.1AFU73604 Torulaspora
franciscae 26S ... 505 e-140
gi4038812gbU72166.1TGU72166 Torulaspora
globosa 26S rib... 505 e-140
gi4038806gbU72160.1ZMU72160
Zygosaccharomyces microelli... 505 e-140
gi4038803gbU72157.1TPU72157 Torulaspora
pretoriensis 26... 505 e-140
gi4038802gbU72156.1TDU72156 Torulaspora
delbrueckii 26S... 505 e-140
gi4038738gbU68548.1KPU68548 Kluyveromyces
polysporus 26... 505 e-140 gi2062314gbU457
88.1PSU45788 Pichia scolyti 26S ribosoma...
505 e-140 gi6683927gbAF202921.1AF202921
Sporopachydermia sp. 91-1... 504 e-140
gi12006162gbAF271085.1AF271085 Candida
ponderosae 26S l... 504 e-140
gi2062272gbU45817.1CSU45817 Candida
sophiae-reginae 26S... 504 e-140
gi4039007gbAF017412.1AF017412 Pichia
lachancei 26S ribo... 500 e-139
gi4038830gbU73581.1PMU73581 Pichia
misumaiensis 26S rib... 500 e-139
gi4038955gbU94934.1PMU94934 Pichia
silvicola 26S riboso... 500 e-139
gi4038896gbU75961.1WMU75961 Williopsis
mucosa 26S ribos... 500 e-139
gi4038762gbU69879.1CSU69879 Candida
silvicultrix 26S ri... 500 e-139
gi4038915gbU84224.1HVU84224 Hanseniaspora
vineae 26S ri... 498 e-138 gi2062276gbU457
74.1CTU45774 Candida tenuis 26S ribosoma...
498 e-138 gi2062275gbU45760.1CTU45760
Candida tenuis 26S ribosoma... 498 e-138
gi12382233gbAF245404.1AF245404 Candida
neerlandica 26S ... 494 e-137
gi11345035gbAF178051.1AF178051 Candida
oleophila strain... 494 e-137
gi4038801gbU71070.1CSU71070 Candida sojae
26S ribosomal... 494 e-137 gi2062308gbU457
66.1PNU45766 Pichia nakazawae var. akita...
494 e-137 gi2062307gbU45748.1PNU45748
Pichia nakazawae var. nakaz... 494 e-137
gi2062274gbU45749.1CTU45749 Candida
tropicalis 26S ribo... 494 e-137
gi4038840gbU74588.1PSU74588 Pichia
silvicola 26S large ... 492 e-136
gi4038829gbU73580.1PEU73580 Pichia
euphorbiae 26S ribos... 492 e-136
gi2062280gbU45752.1CVU45752 Candida
viswanathii 26S rib... 492 e-136
17
4. Algorithms problemsExample 2
GenBank accession BD000079 Candida
boidinii BASE COUNT 189 a 60 c 41 g 228 t ORIGIN
1 taattcaaca agttgtatct ttttttactg ctctttttta
atgatctctc tttatttttt 61 tttcaatcaa tttatttatt
taattttttc acttttataa ttcttgatat gatatgatat 121
gatatgattt tagttctttg tctgtttttt tttttttttt
tcaaactttt cttttaatga 181 ctttatacca aaaattttca
aaaatttcca aaaaaaaaaa caataatgtt ctttttacgt 241
ctctttcctt ttacaaaata tatttattgc ctgcctcatt
tttttcaaat actttttttt 301 ccctgtaaca gtaattagta
aattgaaaaa aataattatt aatttaagta aatagcagca 361
acattgaggt ttacaaatat agtaataata gtctatctac
aaccaatatt aaataatttg 421 atcatttaaa acaacattaa
atttgaaatt tagtacataa ttaataaaag aaaagaggag 481
aaacaaaagc ataataaatc attaaaattt gagtatag
518 bp
18
4. Algorithms problemsExample 2
Score 646 bits (336), Expect 0.0 Identities
379/422 (89) Strand Plus / Plus
Query 97 ataattcttgatatgatatgatatgatatgattttagtt
ctttgtctgnnnnnnnnnnnn 156
S
bjct 97 ataattcttgatatgatatgatatgatatgattttagttct
ttgtctgtttttttttttt 156 Query 157
nnnnncaaacttttcttttaatgactttataccaaaaattttcaaaaatt
tccnnnnnnn 216
Sbjct 157
tttttcaaacttttcttttaatgactttataccaaaaattttcaaaaatt
tccaaaaaaa 216 Query 217 nnnncaataatgttctttttac
gtctctttccttttacaaaatatatttattgcctgcct 276

Sbjct 217 aaaacaataatgttctttttacgt
ctctttccttttacaaaatatatttattgcctgcct 276 Query
277 catttttttcaaatacnnnnnnnnccctgtaacagtaattagtaaa
ttgnnnnnnntaat 336
Sbjct
277 catttttttcaaatacttttttttccctgtaacagtaattagtaaa
ttgaaaaaaataat 336 Query 337
tattaatttaagtaaatagcagcaacattgaggtttacaaatatagtaat
aatagtctat 396
Sbjct 337
tattaatttaagtaaatagcagcaacattgaggtttacaaatatagtaat
aatagtctat 396 Query 397 ctacaaccaatattaaataatt
tgatcatttaaaacaacattaaatttgaaatttagtac 456

Sbjct 397 ctacaaccaatattaaataatttg
atcatttaaaacaacattaaatttgaaatttagtac 456 Query
457 ataattaataaaagaaaagaggagaaacaaaagcataataaatcat
taaaatttgagtat 516
Sbjct
457 ataattaataaaagaaaagaggagaaacaaaagcataataaatcat
taaaatttgagtat 516 Query 517 ag 518
Sbjct 517 ag 518
Score 33.4 bits (17), Expect 222 Identities
17/17 (100) Strand Plus / Plus Query
1taattcaacaagttgta 17 Sbj
ct 1taattcaacaagttgta 17
Saa (379 17)/518 76.5 !!!
19
4. Algorithms problemsExample 2
Score 996 bits (518), Expect 0.0 Identities
518/518 (100), Strand Plus / Plus
Query 1 taattcaacaagttgtatctttttttactgctctttttta
atgatctctctttatttttt 60

Sbjct 1 taattcaacaagttgtatctttttttactg
ctcttttttaatgatctctctttatttttt 60 Query 61
tttcaatcaatttatttatttaattttttcacttttataattcttgatat
gatatgatat 120
Sbjct 61
tttcaatcaatttatttatttaattttttcacttttataattcttgatat
gatatgatat 120 Query 121 gatatgattttagttctttgtc
tgtttttttttttttttttcaaacttttcttttaatga 180

Sbjct 121 gatatgattttagttctttgtctg
tttttttttttttttttcaaacttttcttttaatga 180 Query
181 ctttataccaaaaattttcaaaaatttccaaaaaaaaaaacaataa
tgttctttttacgt 240
Sbjct
181 ctttataccaaaaattttcaaaaatttccaaaaaaaaaaacaataa
tgttctttttacgt 240 Query 241
ctctttccttttacaaaatatatttattgcctgcctcatttttttcaaat
actttttttt 300
Sbjct 241
ctctttccttttacaaaatatatttattgcctgcctcatttttttcaaat
actttttttt 300 Query 301 ccctgtaacagtaattagtaaa
ttgaaaaaaataattattaatttaagtaaatagcagca 360

Sbjct 301 ccctgtaacagtaattagtaaatt
gaaaaaaataattattaatttaagtaaatagcagca 360 Query
361 acattgaggtttacaaatatagtaataatagtctatctacaaccaa
tattaaataatttg 420
Sbjct
361 acattgaggtttacaaatatagtaataatagtctatctacaaccaa
tattaaataatttg 420 Query 421
atcatttaaaacaacattaaatttgaaatttagtacataattaataaaag
aaaagaggag 480
Sbjct 421
atcatttaaaacaacattaaatttgaaatttagtacataattaataaaag
aaaagaggag 480 Query 481 aaacaaaagcataataaatcat
taaaatttgagtatag 518
Sbjct 481
aaacaaaagcataataaatcattaaaatttgagtatag 518
Pairwise alignment without the low complexity
option
Saa 100
20
4. Algorithms problemsExample 3
Solution 1 Since 4 lt 5 lt 8 and 4 lt 6 lt 8 then
Sab 100
OK for Identification
21
4. Algorithms problemsExample 3
5
6
Object a
4
8
Object b
Solution 1 Since 4 lt 5 lt 8 and 4 lt 6 lt 8 then
Sab 100
Solution 2 Dab ((84)/2)-((56)/2) 65.5
0.5 Sab 1-(0.5/6) 91.7
OK for less reliable data
22
4. Algorithms problemsExample 3
5
6
Object a
4
8
Object b
Solution 1 Since 4 lt 5 lt 8 and 4 lt 6 lt 8 then
Sab 100
Solution 2 Dab ((84)/2)-((56)/2) 65.5
0.5 Sab 1-(0.5/6) 91.7
Solution 3 Sab (6-5)/(8-4) 25
OK for reliable data and classification
23
5. BioloMICS Softwareavailable from BioAware,
www.bio-aware.com

• BioloMICS, the Biological Manager for
  Identification, Classification and Statistics

24
5. BioloMICS Softwareavailable from BioAware,
www.bio-aware.com

• BioloMICS, the Biological Manager for
  Identification, Classification and Statistics
• The most complete software solution for the
  storage, the analysis and the publication of
  biological data.

25
5. BioloMICS Softwareavailable from BioAware,
www.bio-aware.com

• BioloMICS, the Biological Manager for
  Identification, Classification and Statistics
• The most complete software solution for the
  storage, the analysis and the publication of
  biological data.
• Virtually any types of data can be properly
  archived and analyzed in BioloMICS databases
• Morphological
• Physiological
• Biochemical
• Chemical
• HPLC, GC, Time series
• Electrophoretical (PCR, RFLP, AFLP, )
• DNA, RNA or protein sequences
• Bibliographical
• Taxonomical
• Geographical
• Pictures, URLs and files of any formats
• Administrative

26
5. BioloMICS Softwareavailable from BioAware,
www.bio-aware.com

• BioloMICS, the Biological Manager for
  Identification, Classification and Statistics
• The most complete software solution for the
  storage, the analysis and the publication of
  biological data.
• Virtually any types of data can be properly
  archived and analyzed in BioloMICS databases
• Morphological
• Physiological
• Biochemical
• Chemical
• HPLC, GC, Time series
• Electrophoretical (PCR, RFLP, AFLP, )
• DNA, RNA or protein sequences
• Bibliographical
• Taxonomical
• Geographical
• Pictures, URLs and files of any formats
• Administrative
• Advanced searching tools allowing complex queries
  and selection of records.

27
5. BioloMICS Softwareavailable from BioAware,
www.bio-aware.com

• BioloMICS, the Biological Manager for
  Identification, Classification and Statistics
• The most complete software solution for the
  storage, the analysis and the publication of
  biological data.
• Virtually any types of data can be properly
  archived and analyzed in BioloMICS databases
• Morphological
• Physiological
• Biochemical
• Chemical
• HPLC, GC, Time series
• Electrophoretical (PCR, RFLP, AFLP, )
• DNA, RNA or protein sequences
• Bibliographical
• Taxonomical
• Geographical
• Pictures, URLs and files of any formats
• Administrative
• Advanced searching tools allowing complex queries
  and selection of records.
• Polyphasic identification, classification and
  correlation analyses,

28
5. BioloMICS Softwareavailable from BioAware,
www.bio-aware.com
Main DB
Relations of (user designed) databases and data
managed with BioloMICS
29
5. BioloMICS Softwareavailable from BioAware,
www.bio-aware.com

• Main multi-users version of the BioloMICS software

30
5. BioloMICS Softwareavailable from BioAware,
www.bio-aware.com

• Main multi-users version of the BioloMICS
  software
• The Internet version of the BioloMICS software,
  see the yeast database at www.cbs.knaw.nl

31
5. BioloMICS Softwareavailable from BioAware,
www.bio-aware.com

• Main multi-users version of the BioloMICS
  software
• The Internet version of the BioloMICS software,
  see the yeast database at www.cbs.knaw.nl
• CDROM/Catalogue

32
6. CBS databases and MycoBank
Yeast species and strains database

• 315 morphological, cultural, physiological,
  sequences data,
• 901 species (soon updated to 1100), 7000
  strains
• First released in July 2000
• www.cbs.knaw.nl/yeast.htm

33
6. CBS databases and MycoBank
Yeast species and strains database

• 315 morphological, cultural, physiological,
  sequences data,
• 901 species (soon updated to 1100), 6000
  strains
• First released in July 2000
• www.cbs.knaw.nl/yeast.htm

Penicillium species (subgenus penicillium)

• 70 morphological, cultural, physiological,
  sequences data,
• 58 species (soon including all (Eu-)Penicillium,
  Talaromyces, Aspergillus and Paecilomyces)
• First released in July 2004
• www.cbs.knaw.nl/penicillium.htm

34
6. CBS databases and MycoBank
Yeast species and strains database

• 315 morphological, cultural, physiological,
  sequences data,
• 901 species (soon updated to 1100), 6000
  strains
• First released in July 2000
• www.cbs.knaw.nl/yeast.htm

Penicillium species (subgenus penicillium)

• 70 morphological, cultural, physiological,
  sequences data,
• 58 species (soon including all (Eu-)Penicillium,
  Talaromyces, Aspergillus and Paecilomyces)
• First released in July 2004
• www.cbs.knaw.nl/penicillium.htm

Phaeoacremonium species database

• 23 morphological and cultural characters were
  coded for the Phaeoacremonium species
• ß-tubulin sequences
• First released in January 2005
• www.cbs.knaw.nl/phaeoacremonium.htm

35
6. CBS databases and MycoBank
Yeast species and strains database

• www.cbs.knaw.nl/yeast.htm

Penicillium species (subgenus penicillium)

• www.cbs.knaw.nl/penicillium.htm

Phaeoacremonium species database

• www.cbs.knaw.nl/phaeoacremonium.htm

MycoBank fungal names and related data bank

• 500.000 fungal names from Kingdom to Species
  levels (lower levels as well)
• All previously published fungal names, unique MB
  ID numbers
• Online searching tool
• Online deposit and modification of new and
  existing data
• Links with GenBank, PubMed, BioloMICS DBs and
  many others
• www.mycobank.org

36
6. CBS databases and MycoBank
Coming databases projects

• Candidemia study project
• Online identification of Medically relevant
  Candida species by electrophoresis methods
• A collaborative work
• Dr. Wieland Meyer, Westmead Hospital, Australia
• Dr. David Ellis, Adelaide Women's and Children's
  Hospital, Australia
• Dr. Laurence Delhaes, Institut Pasteur, France
• Dr. Vincent Robert, CBS, The Netherlands

37
6. CBS databases and MycoBank
Coming databases projects

• Candidemia study project
• Online identification of Medically relevant
  Candida species by electrophoresis methods
• A collaborative work
• Dr. Wieland Meyer, Westmead Hospital, Australia
• Dr. David Ellis, Adelaide Women's and Children's
  Hospital, Australia
• Dr. Laurence Delhaes, Institut Pasteur, France
• Dr. Vincent Robert, CBS, The Netherlands

• Scedosporium project
• Online repository of Scedosporium species and
  related data
• A large collaborative work between many
  institutions

38
6. CBS databases and MycoBank
Coming databases projects

• Candidemia study project
• Online identification of Medically relevant
  Candida species by electrophoresis methods
• A collaborative work
• Dr. Wieland Meyer, Westmead Hospital, Australia
• Dr. David Ellis, Adelaide Women's and Children's
  Hospital, Australia
• Dr. Laurence Delhaes, Institut Pasteur, France
• Dr. Vincent Robert, CBS, The Netherlands

• Scedosporium project
• Online repository of Scedosporium species and
  related data
• A large collaborative work between many
  institutions

• CBS projects
• Aspergillus
• Paecilomyces
• complete Penicillium
• Mycosphaerella and associated genera
• Acremonium
• Black yeasts
• Aphyllophorales

39
6. CBS databases and MycoBank
Coming databases projects

• Candidemia study project
• Online identification of Medically relevant
  Candida species by electrophoresis methods
• A collaborative work
• Dr. Wieland Meyer, Westmead Hospital, Australia
• Dr. David Ellis, Adelaide Women's and Children's
  Hospital, Australia
• Dr. Laurence Delhaes, Institut Pasteur, France
• Dr. Vincent Robert, CBS, The Netherlands

• Scedosporium project
• Online repository of Scedosporium species and
  related data
• A large collaborative work between many
  institutions

• CBS projects
• Aspergillus
• Paecilomyces
• complete Penicillium
• Mycosphaerella and associated genera
• Acremonium
• Black yeasts
• Aphyllophorales

• Open for collaboration !!

40
Conclusion
303 1741, 19 March 2004
gt7000 different regular users for the yeast
database From 96 different countries 500
queries and polyphasic IDs/day
Contact me for a demo after the session
41
Acknowledgements
Meeting organizers Databases Dr. D. Yarrow,
CBS, The Netherlands W. Epping, CBS, The
Netherlands Dr. M.Th. Smith, CBS, The
Netherlands Dr. T. Boekhout, CBS, The
Netherlands Dr. J.A. Stalpers, CBS, The
Netherlands Dr. W. Meyer, Westmead Hospital,
Australia Dr. R. Samson, CBS, The Netherlands Dr.
G. Verkley, CBS, The Netherlands Ir. G.
Stegehuis, CBS, The Netherlands J. Houbraken,
CBS, The Netherlands Dr. P. Crous, CBS, The
Netherlands Dr. S. de Hoog, CBS, The
Netherlands Dr. K. Boundy-Mills, UC Davis,
USA Dr. D. Garcia, Inst. Pasteur, France Dr. F.
Simoens, Inst. Pasteur, Belgium Dr. F. Delhaes,
Inst. Pasteur, France Software Dr. S. Szoke,
BeeComputing, Belgium Dr. W. Meyer, Westmead
Hospital, Australia
Contact Dr. V. Robert Centraalbureau voor
Schimmelcultures, CBS Uppsalalaan 8 3584 CT
Utrecht The Netherlands robert_at_cbs.knaw.nl www.cbs
.knaw.nl BioloMICS Software www.bio-aware.com