Galaxy

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xenTro3
 
xenTro3
  
=== microbes ===
+
=== Microbes ===
  
Staphylococcus_aureus_aureus_USA300_FPR3757
+
* Staphylococcus_aureus_aureus_USA300_FPR3757
Xanthomonas_oryzae_PXO99A
+
* Xanthomonas_oryzae_PXO99A
acidBact_ELLIN345
+
* acidBact_ELLIN345
acidCell_11B
+
* acidCell_11B
acidCryp_JF_5
+
* acidCryp_JF_5
acidJS42
+
* acidJS42
acinSp_ADP1
+
* acinSp_ADP1
actiPleu_L20
+
* actiPleu_L20
aerPer1
+
* aerPer1
aeroHydr_ATCC7966
+
* aeroHydr_ATCC7966
alcaBork_SK2
+
* alcaBork_SK2
alkaEhrl_MLHE_1
+
* alkaEhrl_MLHE_1
anabVari_ATCC29413
+
* anabVari_ATCC29413
anaeDeha_2CP_C
+
* anaeDeha_2CP_C
anapMarg_ST_MARIES
+
* anapMarg_ST_MARIES
aquiAeol
+
* aquiAeol
archFulg1
+
* archFulg1
arthFB24
+
* arthFB24
azoaSp_EBN1
+
* azoaSp_EBN1
azorCaul2
+
* azorCaul2
baciAnth_AMES
+
* baciAnth_AMES
baciHalo
+
* baciHalo
baciSubt
+
* baciSubt
bactThet_VPI_5482
+
* bactThet_VPI_5482
bartHens_HOUSTON_1
+
* bartHens_HOUSTON_1
baumCica_HOMALODISCA
+
* baumCica_HOMALODISCA
bdelBact
+
* bdelBact
bifiLong
+
* bifiLong
blocFlor
+
* blocFlor
bordBron
+
* bordBron
borrBurg
+
* borrBurg
bradJapo
+
* bradJapo
brucMeli
+
* brucMeli
buchSp
+
* buchSp
burk383
+
* burk383
burkCeno_AU_1054
+
* burkCeno_AU_1054
burkCeno_HI2424
+
* burkCeno_HI2424
burkCepa_AMMD
+
* burkCepa_AMMD
burkMall_ATCC23344
+
* burkMall_ATCC23344
burkPseu_1106A
+
* burkPseu_1106A
burkThai_E264
+
* burkThai_E264
burkViet_G4
+
* burkViet_G4
burkXeno_LB400
+
* burkXeno_LB400
caldMaqu1
+
* caldMaqu1
caldSacc_DSM8903
+
* caldSacc_DSM8903
campFetu_82_40
+
* campFetu_82_40
campJeju
+
* campJeju
campJeju_81_176
+
* campJeju_81_176
campJeju_RM1221
+
* campJeju_RM1221
candCars_RUDDII
+
* candCars_RUDDII
candPela_UBIQUE_HTCC1
+
* candPela_UBIQUE_HTCC1
carbHydr_Z_2901
+
* carbHydr_Z_2901
caulCres
+
* caulCres
chlaPneu_CWL029
+
* chlaPneu_CWL029
chlaTrac
+
* chlaTrac
chloChlo_CAD3
+
* chloChlo_CAD3
chloTepi_TLS
+
* chloTepi_TLS
chroSale_DSM3043
+
* chroSale_DSM3043
chroViol
+
* chroViol
clavMich_NCPPB_382
+
* clavMich_NCPPB_382
colwPsyc_34H
+
* colwPsyc_34H
coryEffi_YS_314
+
* coryEffi_YS_314
coxiBurn
+
* coxiBurn
cytoHutc_ATCC33406
+
* cytoHutc_ATCC33406
dechArom_RCB
+
* dechArom_RCB
dehaEthe_195
+
* dehaEthe_195
deinGeot_DSM11300
+
* deinGeot_DSM11300
deinRadi
+
* deinRadi
desuHafn_Y51
+
* desuHafn_Y51
desuPsyc_LSV54
+
* desuPsyc_LSV54
desuRedu_MI_1
+
* desuRedu_MI_1
desuVulg_HILDENBOROUG
+
* desuVulg_HILDENBOROUG
dichNodo_VCS1703A
+
* dichNodo_VCS1703A
ehrlRumi_WELGEVONDEN
+
* ehrlRumi_WELGEVONDEN
ente638
+
* ente638
enteFaec_V583
+
* enteFaec_V583
erwiCaro_ATROSEPTICA
+
* erwiCaro_ATROSEPTICA
erytLito_HTCC2594
+
* erytLito_HTCC2594
eschColi_APEC_O1
+
* eschColi_APEC_O1
eschColi_CFT073
+
* eschColi_CFT073
eschColi_EC4115
+
* eschColi_EC4115
eschColi_EDL933
+
* eschColi_EDL933
eschColi_K12
+
* eschColi_K12
eschColi_MG1655
+
* eschColi_MG1655
eschColi_O157H7
+
* eschColi_O157H7
eschColi_TW14359
+
* eschColi_TW14359
flavJohn_UW101
+
* flavJohn_UW101
franCcI3
+
* franCcI3
franTula_TULARENSIS
+
* franTula_TULARENSIS
fusoNucl
+
* fusoNucl
geobKaus_HTA426
+
* geobKaus_HTA426
geobMeta_GS15
+
* geobMeta_GS15
geobSulf
+
* geobSulf
geobTher_NG80_2
+
* geobTher_NG80_2
geobUran_RF4
+
* geobUran_RF4
gloeViol
+
* gloeViol
glucOxyd_621H
+
* glucOxyd_621H
gramFors_KT0803
+
* gramFors_KT0803
granBeth_CGDNIH1
+
* granBeth_CGDNIH1
haemInfl_KW20
+
* haemInfl_KW20
haemSomn_129PT
+
* haemSomn_129PT
haheChej_KCTC_2396
+
* haheChej_KCTC_2396
halMar1
+
* halMar1
haloHalo1
+
* haloHalo1
haloHalo_SL1
+
* haloHalo_SL1
haloWals1
+
* haloWals1
heliAcin_SHEEBA
+
* heliAcin_SHEEBA
heliHepa
+
* heliHepa
heliPylo_26695
+
* heliPylo_26695
heliPylo_HPAG1
+
* heliPylo_HPAG1
heliPylo_J99
+
* heliPylo_J99
hermArse
+
* hermArse
hypeButy1
+
* hypeButy1
hyphNept_ATCC15444
+
* hyphNept_ATCC15444
idioLoih_L2TR
+
* idioLoih_L2TR
jannCCS1
+
* jannCCS1
lactLact
+
* lactLact
lactPlan
+
* lactPlan
lactSali_UCC118
+
* lactSali_UCC118
lawsIntr_PHE_MN1_00
+
* lawsIntr_PHE_MN1_00
legiPneu_PHILADELPHIA
+
* legiPneu_PHILADELPHIA
leifXyli_XYLI_CTCB0
+
* leifXyli_XYLI_CTCB0
leptInte
+
* leptInte
leucMese_ATCC8293
+
* leucMese_ATCC8293
listInno
+
* listInno
magnMC1
+
* magnMC1
magnMagn_AMB_1
+
* magnMagn_AMB_1
mannSucc_MBEL55E
+
* mannSucc_MBEL55E
mariAqua_VT8
+
* mariAqua_VT8
mariMari_MCS10
+
* mariMari_MCS10
mculMari1
+
* mculMari1
mesoFlor_L1
+
* mesoFlor_L1
mesoLoti
+
* mesoLoti
metAce1
+
* metAce1
metMar1
+
* metMar1
metaSedu
+
* metaSedu
methAeol1
+
* methAeol1
methBark1
+
* methBark1
methBoon1
+
* methBoon1
methBurt2
+
* methBurt2
methCaps_BATH
+
* methCaps_BATH
methFlag_KT
+
* methFlag_KT
methHung1
+
* methHung1
methJann1
+
* methJann1
methKand1
+
* methKand1
methLabrZ_1
+
* methLabrZ_1
methMari_C5_1
+
* methMari_C5_1
methMari_C7
+
* methMari_C7
methMaze1
+
* methMaze1
methPetr_PM1
+
* methPetr_PM1
methSmit1
+
* methSmit1
methStad1
+
* methStad1
methTher1
+
* methTher1
methTherPT1
+
* methTherPT1
methVann1
+
* methVann1
moorTher_ATCC39073
+
* moorTher_ATCC39073
mycoGeni
+
* mycoGeni
mycoTube_H37RV
+
* mycoTube_H37RV
myxoXant_DK_1622
+
* myxoXant_DK_1622
nanEqu1
+
* nanEqu1
natrPhar1
+
* natrPhar1
neisGono_FA1090_1
+
* neisGono_FA1090_1
neisMeni_FAM18_1
+
* neisMeni_FAM18_1
neisMeni_MC58_1
+
* neisMeni_MC58_1
neisMeni_Z2491_1
+
* neisMeni_Z2491_1
neorSenn_MIYAYAMA
+
* neorSenn_MIYAYAMA
nitrEuro
+
* nitrEuro
nitrMult_ATCC25196
+
* nitrMult_ATCC25196
nitrOcea_ATCC19707
+
* nitrOcea_ATCC19707
nitrWino_NB_255
+
* nitrWino_NB_255
nocaFarc_IFM10152
+
* nocaFarc_IFM10152
nocaJS61
+
* nocaJS61
nostSp
+
* nostSp
novoArom_DSM12444
+
* novoArom_DSM12444
oceaIhey
+
* oceaIhey
oenoOeni_PSU_1
+
* oenoOeni_PSU_1
onioYell_PHYTOPLASMA
+
* onioYell_PHYTOPLASMA
orieTsut_BORYONG
+
* orieTsut_BORYONG
paraDeni_PD1222
+
* paraDeni_PD1222
paraSp_UWE25
+
* paraSp_UWE25
pastMult
+
* pastMult
pediPent_ATCC25745
+
* pediPent_ATCC25745
peloCarb
+
* peloCarb
peloLute_DSM273
+
* peloLute_DSM273
peloTher_SI
+
* peloTher_SI
photLumi
+
* photLumi
photProf_SS9
+
* photProf_SS9
picrTorr1
+
* picrTorr1
pireSp
+
* pireSp
polaJS66
+
* polaJS66
polyQLWP
+
* polyQLWP
porpGing_W83
+
* porpGing_W83
procMari_CCMP1375
+
* procMari_CCMP1375
propAcne_KPA171202
+
* propAcne_KPA171202
pseuAeru
+
* pseuAeru
pseuHalo_TAC125
+
* pseuHalo_TAC125
psycArct_273_4
+
* psycArct_273_4
psycIngr_37
+
* psycIngr_37
pyrAby1
+
* pyrAby1
pyrAer1
+
* pyrAer1
pyrFur2
+
* pyrFur2
pyrHor1
+
* pyrHor1
pyroArse1
+
* pyroArse1
pyroCali1
+
* pyroCali1
pyroIsla1
+
* pyroIsla1
ralsEutr_JMP134
+
* ralsEutr_JMP134
ralsSola
+
* ralsSola
rhizEtli_CFN_42
+
* rhizEtli_CFN_42
rhodPalu_CGA009
+
* rhodPalu_CGA009
rhodRHA1
+
* rhodRHA1
rhodRubr_ATCC11170
+
* rhodRubr_ATCC11170
rhodSpha_2_4_1
+
* rhodSpha_2_4_1
rickBell_RML369_C
+
* rickBell_RML369_C
roseDeni_OCH_114
+
* roseDeni_OCH_114
rubrXyla_DSM9941
+
* rubrXyla_DSM9941
saccDegr_2_40
+
* saccDegr_2_40
saccEryt_NRRL_2338
+
* saccEryt_NRRL_2338
saliRube_DSM13855
+
* saliRube_DSM13855
saliTrop_CNB_440
+
* saliTrop_CNB_440
salmEnte_PARATYPI_ATC
+
* salmEnte_PARATYPI_ATC
salmTyph
+
* salmTyph
salmTyph_TY2
+
* salmTyph_TY2
shewANA3
+
* shewANA3
shewAmaz
+
* shewAmaz
shewBalt
+
* shewBalt
shewDeni
+
* shewDeni
shewFrig
+
* shewFrig
shewLoihPV4
+
* shewLoihPV4
shewMR4
+
* shewMR4
shewMR7
+
* shewMR7
shewOnei
+
* shewOnei
shewPutrCN32
+
* shewPutrCN32
shewW318
+
* shewW318
shigFlex_2A
+
* shigFlex_2A
siliPome_DSS_3
+
* siliPome_DSS_3
sinoMeli
+
* sinoMeli
sodaGlos_MORSITANS
+
* sodaGlos_MORSITANS
soliUsit_ELLIN6076
+
* soliUsit_ELLIN6076
sphiAlas_RB2256
+
* sphiAlas_RB2256
stapAure_MU50
+
* stapAure_MU50
stapMari1
+
* stapMari1
streCoel
+
* streCoel
strePyog_M1_GAS
+
* strePyog_M1_GAS
sulSol1
+
* sulSol1
sulfAcid1
+
* sulfAcid1
sulfToko1
+
* sulfToko1
symbTher_IAM14863
+
* symbTher_IAM14863
synePCC6
+
* synePCC6
syneSp_WH8102
+
* syneSp_WH8102
syntAcid_SB
+
* syntAcid_SB
syntFuma_MPOB
+
* syntFuma_MPOB
syntWolf_GOETTINGEN
+
* syntWolf_GOETTINGEN
therAcid1
+
* therAcid1
therElon
+
* therElon
therFusc_YX
+
* therFusc_YX
therKoda1
+
* therKoda1
therMari
+
* therMari
therPend1
+
* therPend1
therPetr_RKU_1
+
* therPetr_RKU_1
therTeng
+
* therTeng
therTher_HB27
+
* therTher_HB27
therTher_HB8
+
* therTher_HB8
therVolc1
+
* therVolc1
thioCrun_XCL_2
+
* thioCrun_XCL_2
thioDeni_ATCC25259
+
* thioDeni_ATCC25259
thioDeni_ATCC33889
+
* thioDeni_ATCC33889
trepPall
+
* trepPall
tricEryt_IMS101
+
* tricEryt_IMS101
tropWhip_TW08_27
+
* tropWhip_TW08_27
uncuMeth_RCI
+
* uncuMeth_RCI
ureaUrea
+
* ureaUrea
vermEise_EF01_2
+
* vermEise_EF01_2
vibrChol1
+
* vibrChol1
vibrChol_O395_1
+
* vibrChol_O395_1
vibrFisc_ES114_1
+
* vibrFisc_ES114_1
vibrPara1
+
* vibrPara1
vibrVuln_CMCP6_1
+
* vibrVuln_CMCP6_1
vibrVuln_YJ016_1
+
* vibrVuln_YJ016_1
wiggBrev
+
* wiggBrev
wolbEndo_OF_DROSOPHIL
+
* wolbEndo_OF_DROSOPHIL
woliSucc
+
* woliSucc
xantCamp
+
* xantCamp
xyleFast
+
* xyleFast
yersPest_CO92
+
* yersPest_CO92
zymoMobi_ZM4
+
* zymoMobi_ZM4
  
  
 
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
 
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]

Revision as of 16:08, 7 March 2013

Contents


Overview

The UAB Galaxy platform for experimental biology and comparative genomics designed to help you analyze multiple alignments, compare genomic annotations, profile metagenomic samples and more from your web browser. This platform is built on Galaxy, backed by the Cheaha compute cluster, and powered by UABgrid.

The primary uses of UAB Galaxy are to provide a simple web interface for NGS (short read sequencing) analysis for genomic and transcriptomic datasets, using tools like BWA, Bowtie, Tophat and Cufflinks, as well as simple sequence manipulation via the EMBOSS toolkit.

Using Galaxy / Tutorials

There are numerous general tutorials online at the Penn State public Galaxy site that are worth looking at.

There are also several UAB tutorials on NGS Analysis with Galaxy, created for HPC Boot Camp 2011 and a nice talk by Jeremy Goecks during Research Computing Day 2011.

Support

UAB galaxy-users list-serv: subscribe search.

UAB galaxy-help list-serv: [1] to contact admins of the UAB galaxy instance.

Privacy

Note that your data will be stored on the cluster filesystem, and while not accessible to ordinary users, it can be easily accessed by any of the galaxy or cluster administrators. It is not encrypted. Do not store sensitive information in this system.

Galaxy@UAB

The UAB Galaxy instance can be accessed at https://galaxy.uabgrid.uab.edu using BlazerID credentials. No account on the cluster is needed. However, the tools installed for galaxy (BWA, etc) can be accessed via the command line if you have an account on the cluster.

Available Tools

Following is a partial list highlighting some of the important tools available. Additional tools can be installed upon request. To search for tools already integrated into the Galaxy system, see the Galaxy ToolShed.


Software Version Information
bwa 0.5.9-r26 Align genomic short reads to a reference genome
bowtie 0.12.7 Align genomic short reads to a reference genome
samtools 0.1.12a Alignment (SAM/BAM file) manipulations
velvet 1.1.03 Denovo Assembly
Top Hat 1.4.0 Align transcriptome short reads to a reference genome
Cuff Links 1.3.0 Reconstruct and quantify transcript levels from tophat alignments.
EMBOSS 6.3.1 European Molecular Biology Open Software Suite - sequence manipulation and format conversion


Installed Genome Indexes

You can always use your own genome by uploading the .fasta into your history, but alignments against installed (pre-indexed) genomes run much more quickly. If you need an additional genome installed, please contact [2].

dbkey Genome Accessions
mm9 Mouse July 2007 (NCBI37/mm9) (mm9)
mm10 Mouse Dec. 2011 (GRCm38/mm10) (mm10)
hg18 Human Mar. 2006 (NCBI36/hg18) (hg18)
hg19 Human Feb. 2009 (GRCh37/hg19) (hg19)
sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)
sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)
ce10 C. elegans Oct. 2010 (WS220/ce10) (ce10)
rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4)
rn5 Rat Mar. 2012 (RGSC 5.0/rn5) (rn5)
danRer7 Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7)
eschColi_APEC_O1 Escherichia coli APEC O1 chr=5082025
eschColi_CFT073 Escherichia coli CFT073 chr=5231428
eschColi_EC4115 Escherichia coli EC4115 chr=5572075,plasmid_pO157=94644,plasmid_pEC4115=37452
eschColi_K12 Escherichia coli K12 chr=4639675
eschColi_EDL993 Escherichia coli O157:H7 EDL933 NC_007414=92077,NC_002655=5528445
eschColi_O157H7 Escherichia coli O157:H7 EDL933 NC_007414=92077,NC_002655=5528445
eschColi_TW14359 Escherichia coli TW14359 chr=5528136,plasmid_pO157=94601

Additional Genomes that can be quickly installed

These are pre-indexed genomes we can easily download from Penn State's Galaxy Data-Cache

Organisms

AaegL1 Acropora_digitifera AgamP3 Arabidopsis_thaliana_TAIR10 Arabidopsis_thaliana_TAIR9 Araly1 Bombyx_mori_p50T_2.0 CpipJ1 Homo_sapiens_AK1 Homo_sapiens_nuHg19_mtrCRS Hydra_JCVI IscaW1 PhumU1 Physcomitrella_patens_patens Ptrichocarpa_156 Saccharomyces_cerevisiae_S288C_SGD2010 Schizosaccharomyces_pombe_1.1 Spur_v2.6 Sscrofa9.58 Tcacao_1.0 Tcas_3.0 Theobroma_cocoa Zea_mays_B73_RefGen_v2 ailMel1 anoCar1 anoCar2 anoGam1 apiMel1 apiMel2 apiMel3 apiMel4.5 aplCal1 bighorn_sheep borEut13 bosTau2 bosTau3 bosTau4 bosTau5 bosTau6 bosTau7 bosTauMd3 braFlo1 caeJap1 caePb1 caePb2 caeRem2 caeRem3 calJac1 calJac3 canFam1 canFam2 canFam3 cavPor2 cavPor3 cb3 ce10 ce2 ce3 ce4 ce5 ce6 ce7 ce8 ce9 choHof1 chrPic1 ci2 danRer2 danRer3 danRer4 danRer5 danRer6 danRer7 dasNov1 dasNov2 dipOrd1 dm1 dm2 dm3 dp3 dp4 droAna1 droAna2 droAna3 droEre1 droEre2 droGri1 droGri2 droMoj1 droMoj2 droMoj3 droPer1 droSec1 droSim1 droVir1 droVir2 droVir3 droWil1 droYak1 droYak2 echTel1 emf equCab1 equCab2 equCab2_chrM eriEur1 felCat3 felCat4 fr1 fr2 fr3 galGal2 galGal3 galGal4 gasAcu1 geoFor1 gorGor1 gorGor3 hetGla1 hetGla2 hg16 hg17 hg18 hg19 hg_g1k_v37 lMaj5 lengths loxAfr3 loxAfr4 macEug1 melGal1 melUnd1 micMur1 mm10 mm5 mm6 mm7 mm8 mm9 monDom4 monDom5 myoLuc1 myoLuc2 nomLeu1 nomLeu2 ochPri2 ornAna1 oryCun1 oryCun2 oryLat1 oryLat2 oryza_sativa_japonica_nipponbare_IRGSP4.0 otoGar1 oviAri1 pUC18 panTro1 panTro2 panTro3 papHam1 petMar1 phiX ponAbe2 priPac1 rheMac2 rheMac3 rn3 rn4 rn5 sacCer1 sacCer2 sacCer3 sarHar1 sorAra1 strPur2 strPur3 susScr2 susScr3 taeGut1 tarSyr1 tetNig1 tetNig2 triCas2 tupBel1 venter1 xenTro1 xenTro2 xenTro3

Microbes

  • Staphylococcus_aureus_aureus_USA300_FPR3757
  • Xanthomonas_oryzae_PXO99A
  • acidBact_ELLIN345
  • acidCell_11B
  • acidCryp_JF_5
  • acidJS42
  • acinSp_ADP1
  • actiPleu_L20
  • aerPer1
  • aeroHydr_ATCC7966
  • alcaBork_SK2
  • alkaEhrl_MLHE_1
  • anabVari_ATCC29413
  • anaeDeha_2CP_C
  • anapMarg_ST_MARIES
  • aquiAeol
  • archFulg1
  • arthFB24
  • azoaSp_EBN1
  • azorCaul2
  • baciAnth_AMES
  • baciHalo
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  • bartHens_HOUSTON_1
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  • bdelBact
  • bifiLong
  • blocFlor
  • bordBron
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  • bradJapo
  • brucMeli
  • buchSp
  • burk383
  • burkCeno_AU_1054
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  • burkCepa_AMMD
  • burkMall_ATCC23344
  • burkPseu_1106A
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  • burkXeno_LB400
  • caldMaqu1
  • caldSacc_DSM8903
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  • chlaPneu_CWL029
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  • nanEqu1
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  • nitrEuro
  • nitrMult_ATCC25196
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  • nitrWino_NB_255
  • nocaFarc_IFM10152
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  • nostSp
  • novoArom_DSM12444
  • oceaIhey
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  • paraDeni_PD1222
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  • rhodRubr_ATCC11170
  • rhodSpha_2_4_1
  • rickBell_RML369_C
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  • rubrXyla_DSM9941
  • saccDegr_2_40
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  • saliRube_DSM13855
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  • shigFlex_2A
  • siliPome_DSS_3
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  • soliUsit_ELLIN6076
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  • therAcid1
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  • thioCrun_XCL_2
  • thioDeni_ATCC25259
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  • trepPall
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  • yersPest_CO92
  • zymoMobi_ZM4
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