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We would like to
present an automated pipeline, AUGUR,
which integrates multiple computational tools for surface protein prediction and
functional classification of proteins from gram-positive bacteria.
Augur consists of tools for identifying
all major surface proteins, through signal peptide prediction, transmembrane
protein prediction and all types of surface anchors e.g. lipoproteins or LPXTG proteins.
It also annotates the genome using the SCOP protein
structural database, and the COG functional classification.
Augur update
Posted by Andre |
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Monday 07 September 2009
current update with 216 organisms is done!
enclosed an overview of the bacteria included in the new version:
Acidothermus cellulolyticus 11B
Arthrobacter aurescens TC1
Arthrobacter FB24
Aster yellows witches-broom phytoplasma
Bacillus amyloliquefaciens FZB42
Bacillus anthracis Ames Ancestor 0581
Bacillus anthracis Ames
Bacillus anthracis str Sterne
Bacillus cereus 03BB102
Bacillus cereus AH187
Bacillus cereus AH820
Bacillus cereus ATCC 10987
Bacillus cereus ATCC 14579
Bacillus cereus B4264
Bacillus cereus cytotoxis NVH 391-98
Bacillus cereus G9842
Bacillus cereus Q1
Bacillus cereus ZK
Bacillus clausii KSM-K16
Bacillus halodurans
Bacillus licheniformis ATCC 14580
Bacillus licheniformis DSM 13
Bacillus subtilis 168
Bacillus thuringiensis Al Hakam
Bacillus thuringiensis konkukian
Bacillus weihenstephanensis KBAB4
Bifidobacterium adolescentis ATCC 15703
Bifidobacterium animalis lactis AD011
Bifidobacterium longum
Bifidobacterium longum DJO10A
Bifidobacterium longum infantis ATCC 15697
Bifidobacterium longum
Campylobacter jejuni
Carboxydothermus hydrogenoformans Z-2901
Clostridium acetobutylicum
Clostridium acetobutylicum
Clostridium beijerinckii NCIMB 8052
Clostridium botulinum A3 Loch Maree
Clostridium botulinum A ATCC 19397
Clostridium botulinum A Hall
Clostridium botulinum A
Clostridium botulinum B1 Okra
Clostridium botulinum B Eklund 17B
Clostridium botulinum E3 Alaska E43
Clostridium botulinum F Langeland
Clostridium cellulolyticum H10
Clostridium difficile 630
Clostridium difficile QCD-32g58
Clostridium kluyveri DSM 555
Clostridium kluyveri NBRC 12016
Clostridium novyi NT
Clostridium perfringens ATCC 13124
Clostridium perfringens
Clostridium perfringens SM101
Clostridium phytofermentans ISDg
Clostridium tetani E88
Clostridium thermocellum ATCC 27405
Colwellia psychrerythraea 34H
Coprothermobacter proteolyticus DSM 5265
Corynebacterium diphtheriae
Corynebacterium efficiens YS-314
Corynebacterium glutamicum ATCC 13032 Bielefeld
Corynebacterium glutamicum ATCC 13032 Kitasato
Corynebacterium glutamicum R
Corynebacterium jeikeium K411
Corynebacterium urealyticum DSM 7109
Desulfitobacterium hafniense Y51
Enterococcus faecalis V583
Frankia alni ACN14a
Frankia CcI3
Geobacillus kaustophilus HTA426
Geobacillus thermodenitrificans NG80-2
Halothermothrix orenii H 168
Heliobacterium modesticaldum Ice1
Kineococcus radiotolerans SRS30216
Lactobacillus acidophilus NCFM
Lactobacillus brevis ATCC 367
Lactobacillus casei ATCC 334
Lactobacillus casei
Lactobacillus delbrueckii bulgaricus ATCC BAA-365
Lactobacillus delbrueckii bulgaricus
Lactobacillus fermentum IFO 3956
Lactobacillus gasseri ATCC 33323
Lactobacillus helveticus DPC 4571
Lactobacillus johnsonii NCC 533
Lactobacillus plantarum
Lactobacillus reuteri DSM 20016
Lactobacillus reuteri F275 Kitasato
Lactobacillus sakei 23K
Lactobacillus salivarius UCC118
Lactococcus lactis cremoris MG1363
Lactococcus lactis cremoris SK11
Lactococcus lactis
Leifsonia xyli xyli
Listeria innocua
Listeria monocytogenes 12a F6854
Listeria monocytogenes 4b F2365
Listeria monocytogenes 4b H7858
Listeria monocytogenes EGDe
Listeria welshimeri serovar 6b SLCC5334
Mesoplasma florum L1
Moorella thermoacetica ATCC 39073
Mycobacterium abscessus ATCC 19977T
Mycobacterium avium 104
Mycobacterium avium paratuberculosis
Mycobacterium bovis BCG Pasteur 1173P2
Mycobacterium bovis BCG Tokyo 172
Mycobacterium bovis
Mycobacterium gilvum PYR-GCK
Mycobacterium JLS
Mycobacterium KMS
Mycobacterium leprae
Mycobacterium marinum M
Mycobacterium MCS
Mycobacterium smegmatis MC2 155
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis F11
Mycobacterium tuberculosis H37Ra
Mycobacterium tuberculosis H37Rv
Mycobacterium ulcerans Agy99
Mycobacterium vanbaalenii PYR-1
Mycoplasma agalactiae PG2
Mycoplasma arthritidis 158L3 1
Mycoplasma capricolum ATCC 27343
Mycoplasma gallisepticum
Mycoplasma genitalium
Mycoplasma hyopneumoniae 232
Mycoplasma hyopneumoniae 7448
Mycoplasma hyopneumoniae J
Mycoplasma mobile 163K
Mycoplasma mycoides
Mycoplasma penetrans
Mycoplasma pneumoniae
Mycoplasma pulmonis
Mycoplasma synoviae 53
Nocardia farcinica IFM10152
Nocardioides JS614
Oceanobacillus iheyensis
Oenococcus oeni PSU-1
Onion yellows phytoplasma
Propionibacterium acnes KPA171202
Rhodococcus RHA1
Rubrobacter xylanophilus DSM 9941
Saccharopolyspora erythraea NRRL 2338
Salinispora tropica CNB-440
Staphylococcus aureus aureus MRSA252
Staphylococcus aureus aureus MSSA476
Staphylococcus aureus COL
Staphylococcus aureus JH1
Staphylococcus aureus JH9
Staphylococcus aureus Mu3
Staphylococcus aureus Mu50
Staphylococcus aureus MW2
Staphylococcus aureus N315
Staphylococcus aureus NCTC 8325
Staphylococcus aureus Newman
Staphylococcus aureus RF122
Staphylococcus aureus USA300
Staphylococcus aureus USA300 TCH1516
Staphylococcus carnosus TM300
Staphylococcus epidermidis ATCC 12228
Staphylococcus epidermidis RP62A
Staphylococcus haemolyticus
Staphylococcus saprophyticus
Streptococcus agalactiae 2603
Streptococcus agalactiae A909
Streptococcus agalactiae NEM316
Streptococcus equi 4047
Streptococcus equi zooepidemicus MGCS10565
Streptococcus equi zooepidemicus
Streptococcus gordonii Challis substr CH1
Streptococcus mutans
Streptococcus pneumoniae 70585
Streptococcus pneumoniae ATCC 700669
Streptococcus pneumoniae CGSP14
Streptococcus pneumoniae D39
Streptococcus pneumoniae G54
Streptococcus pneumoniae Hungary19A 6
Streptococcus pneumoniae JJA
Streptococcus pneumoniae P1031
Streptococcus pneumoniae R6
Streptococcus pneumoniae Taiwan19F 14
Streptococcus pneumoniae TIGR4
Streptococcus pyogenes M1 GAS
Streptococcus pyogenes Manfredo
Streptococcus pyogenes MGAS10270
Streptococcus pyogenes MGAS10394
Streptococcus pyogenes MGAS10750
Streptococcus pyogenes MGAS2096
Streptococcus pyogenes MGAS315
Streptococcus pyogenes MGAS5005
Streptococcus pyogenes MGAS6180
Streptococcus pyogenes MGAS8232
Streptococcus pyogenes MGAS9429
Streptococcus pyogenes NZ131
Streptococcus pyogenes SF370 serotype M1
Streptococcus pyogenes SSI-1
Streptococcus sanguinis SK36
Streptococcus suis 05ZYH33
Streptococcus suis 98HAH33
Streptococcus thermophilus CNRZ1066
Streptococcus thermophilus LMD-9
Streptococcus thermophilus LMG 18311
Streptococcus uberis 0140J
Streptomyces avermitilis
Streptomyces coelicolor
Streptomyces griseus NBRC 13350
Thermoanaerobacter tengcongensis
Thermobifida fusca YX
Tropheryma whipplei TW08 27
Tropheryma whipplei Twist
Ureaplasma parvum serovar 3 ATCC 27815
Ureaplasma urealyticum serovar 10 ATCC 33699
Ureaplasma urealyticum
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