[Seqinr-commits] r1828 - in pkg: R inst/sequences man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 27 15:50:55 CET 2014
Author: simonpenel
Date: 2014-11-27 15:50:55 +0100 (Thu, 27 Nov 2014)
New Revision: 1828
Removed:
pkg/inst/sequences/goldtable15Dec07.txt
Modified:
pkg/R/dia.bactgensize.R
pkg/man/dia.bactgensize.Rd
Log:
Now goldtable15Dec07 is available on the ftp of pbil
Modified: pkg/R/dia.bactgensize.R
===================================================================
--- pkg/R/dia.bactgensize.R 2014-11-27 11:18:53 UTC (rev 1827)
+++ pkg/R/dia.bactgensize.R 2014-11-27 14:50:55 UTC (rev 1828)
@@ -1,7 +1,7 @@
dia.bactgensize <- function(
fit = 2, p = 0.5, m1 = 2000, sd1 = 600, m2 = 4500, sd2 = 1000, p3 = 0.05,
m3 = 9000, sd3 = 1000, maxgensize = 20000,
- source = c(system.file("sequences/goldtable15Dec07.txt", package = "seqinr"),
+ source = c("ftp://pbil.univ-lyon1.fr/pub/seqinr/data/goldtable15Dec07.txt",
"http://www.genomesonline.org/DBs/goldtable.txt"))
{
#
@@ -11,7 +11,7 @@
#
# Build source of data string:
#
- if(source == system.file("sequences/goldtable15Dec07.txt", package = "seqinr")){
+ if(source == "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/goldtable15Dec07.txt"){
sodtxt <- "Source of data: GOLD (Genomes OnLine Database) 15 Dec 2007"
} else {
sodtxt <- paste("Source of data: GOLD (Genomes OnLine Database)",date())
Deleted: pkg/inst/sequences/goldtable15Dec07.txt
===================================================================
--- pkg/inst/sequences/goldtable15Dec07.txt 2014-11-27 11:18:53 UTC (rev 1827)
+++ pkg/inst/sequences/goldtable15Dec07.txt 2014-11-27 14:50:55 UTC (rev 1828)
@@ -1,3126 +0,0 @@
-SUPERKINGDOM PHYLUM CLASS ORDER FAMILY GENUS SPECIES DOMAIN Organism STRAIN SEROVAR SEQUENCING METHOD SEQUENCING DEPTH STRAININFO Culture SYMBIONT TYPE PHYLOGENY SEQUENCING STATUS PROJECT STATUS PHENOTYPE RELEVANCE DISEASE HABITAT PH TEMPERATURE ISOLATION COUNTRY GC(%) AVAILABILITY GOLDSTAMP GOLDSTAMP OLD GREENGENES ID GCAT ID TAXON ID ENTREZ PID IMG OID SIZE(kb) ORFs CHROMOSOMES PLASMIDS DATA DATABASES INSTITUTE FUNDING PUBLICATION DATE CONTACT NAME CONTACT EMAIL
-Bacteria Thermotogae Thermotogales Thermotogaceae Petrotoga Petrotoga mobilis BACTERIAL Petrotoga mobilis SJ95t ABI, 454 11.4x Genome THERMOTOGAE Complete complete Rod-shaped, Thermophile, Anaerobe, Halotolerant, Motile, Nonsporulating Evolutionary, Biotechnological, Oil industry None Marine, Oil fields Production waters of a North Sea oil reservoir USA 34.1 Public Gc00684 Gi01028 001358_GCAT 403833 17679 640612213 2169 1898 1 0 NC_010003 NCBI Joint Genome Institute DOE Unpublished November 21, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Proteobacteria Burkholderiales Comamonadaceae Delftia Delftia acidovorans BACTERIAL Delftia acidovorans SPH-1 ABI 12.8x ATCC 15668 Genome PROTEOBACTERIA-BETA Complete complete Aerobe, Mesophile Biotechnological, Wastewater treatment, Oil industry None Soil, Sludge, Oil fields, Aquatic 30 Soil enriched with acetamide in Delft in the Netherlands USA 66 Public Gc00683 Gi01332 001744_GCAT 398578 17413 639857025 6767 6040 1 0 NC_010002 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished November 21, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Firmicutes Clostridiales Clostridiaceae Clostridium Clostridium phytofermentans BACTERIAL Clostridium phytofermentans ISDg ABI 13x ATCC 700394 Genome FIRMICUTES Complete complete Anaerobe, Cellulolytic, Motile, Rod-shaped, Mesophile, Sporulating Biotechnological, Hydrogen production, Ethanol production, Energy production, Ecological None Soil 37 Forest soil near the Quabbin Reservoir in Massachusetts USA 35.9 Public Gc00682 Gi00162 000967_GCAT 357809 16184 638341067 4847 3902 1 0 NC_010001 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished November 21, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Proteobacteria Alteromonadales Shewanellaceae Shewanella Shewanella baltica BACTERIAL Shewanella baltica OS195 ABI 10x Genome PROTEOBACTERIA-GAMMA Complete complete Anaerobe, Rod-shaped, Motile, Facultative Biotechnological None Marine 4 Baltic Sea USA 46 Public Gc00681 Gi00964 001489_GCAT 399599 13389 638341189 5347 4499 1 3 NC_009997 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished November 21, 2007 Richardson P microbes at cuba.jgi-psf.org
-Eukaryota unclassified unclassified unclassified Hemiselmis Hemiselmis andersenii EUKARYAL Hemiselmis andersenii CCMP644 (nucleomorph) Genome PROTISTS Complete complete Evolutionary Canada Public Gc00680 002361_GCAT 464988 571 3 NC_009977, NC_009978, NC_009979 Dalhousie Univ PNAS in press November 16, 2007 Archibald JM http://myweb.dal.ca/jmarchib/
-Bacteria Cyanobacteria Prochlorales Prochlorococcaceae Prochlorococcus Prochlorococcus marinus BACTERIAL Prochlorococcus marinus MIT 9211 ABI Genome CYANOBACTERIA Complete complete Nonmotile, Carbon cycle, Mesophile Environmental, MMI None Marine Equatorial Pacific at a depth of 83m USA 39 Public Gc00679 Gi00872 001368_GCAT 93059 13551 638341154 1688 1855 1 0 NC_009976 NCBI, JCVI J Craig Venter Institute, MIT Moore Foundation Unpublished November 13, 2007 Chisholm S http://csbi.mit.edu/faculty/Members/PennyChisholm
-Archaea Euryarchaeota Methanococcales Methanococcaceae Methanococcus Methanococcus maripaludis ARCHAEAL Methanococcus maripaludis C6 Genome EURYARCHAEOTA-METHANOCOCCI Complete complete Methanogen, Motile, Obligate anaerobe, Nonsporulating, Hydrogenotrophic, Nitrogen fixation, Lithotroph, Mesophile Biotechnological, Energy production None Aquatic, Sediment 6.5 - 8 20 - 45 Intertidal sediments USA 33 Public Gc00678 Gi01307 001820_GCAT 444158 19639 1744 1826 1 0 NC_009975 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished November 13, 2007 Whitman WB whitman at uga.edu
-Bacteria Chloroflexi Herpetosiphonales Herpetosiphonaceae Herpetosiphon Herpetosiphon aurantiacus BACTERIAL Herpetosiphon aurantiacus ATCC 23779 ABI 11x DSM 785, ATCC 23779 Genome CHLOROFLEXI Complete complete Filament-shaped, Motile, Aerobe, Mesophile Biotechnological None Aquatic Birch Lake in Minnesota USA 50 Public Gc00677 Gi00947 001142_GCAT 316274 16523 638341105 6346 4976 1 2 NC_009972 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished November 13, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Proteobacteria Myxococcales Polyangiaceae Sorangium Sorangium cellulosum BACTERIAL Sorangium (Polyangium) cellulosum So ce56 Genome PROTEOBACTERIA-DELTA Complete complete Biotechnological None Germany Public Gc00676 Gi00561 001504_GCAT 56 13033 Bielefeld Univ Bielefeld Univ BMBF Nat Biotechnol. Epub October 28, 2007 Muller R rom at mx.uni-saarland.de
-Eukaryota Ascomycota Saccharomycetales unclassified Candida Candida albicans EUKARYAL Candida albicans SC5314 ABI 10.9x Genome FUNGI-ASCOMYCOTA Quality Draft complete Pathogen Medical, Human Pathogen Oral infection, Vaginal infection USA Public Gc00675 Gi00126 001975_GCAT 237561 10701 640281004 14855 6354 8 0 AACQ00000000 NCBI, Stanford Univ, Institut Pasteur, CandidaDB Stanford Univ Burroughs Wellcome Fund, NIH-NIDCR PNAS 101, 7329-34 May 11, 2004 Davis RW Dbowe at sequence.stanford.edu
-Archaea Crenarchaeota Thermoproteales Thermoproteaceae Caldivirga Caldivirga maquilingensis ARCHAEAL Caldivirga maquilingensis IC-167 ABI DSM 13496 Genome CRENARCHAEOTA-THERMOPROTEI Complete complete Hyperthermophile, Heterotroph, Aerobe, Rod-shaped, Nonmotile, Nonsporulating Biotechnological None Aquatic 85 Acidic hot spring in the Philippines USA 43 Public Gc00674 Gi01059 001815_GCAT 397948 17421 640196211 2077 1963 1 0 NC_009954 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished October 5, 2007 House C chouse at geosc.psu.edu
-Bacteria Actinobacteria Actinomycetales Micromonosporaceae Salinispora Salinispora arenicola BACTERIAL Salinispora arenicola CNS205 ABI 11.4x Genome ACTINOBACTERIA Complete complete Filament-shaped, Sporulating, Motile, Aerobe, Mesophile Biotechnological, Medical, Cancer treatment None Aquatic, Marine, Sediment Beach sand at a depth of 1 meter from Sweetings Cay in the Bahamas USA 69.5 Public Gc00673 Gi01541 001441_GCAT 391037 17109 639857040 5786 4917 1 0 NC_009953 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished October 5, 2007 Jensen P pjensen at ucsd.edu
-Bacteria Proteobacteria Desulfobacterales Desulfobacteraceae Desulfococcus Desulfococcus oleovorans BACTERIAL Desulfococcus oleovorans Hxd3 ABI, 454 12x DSM 6200 Genome PROTEOBACTERIA-DELTA Complete complete Sulfate reducer, Alkane degrader, Nonmotile, Nonsporulating, Coccus-shaped, Anaerobe, Mesophile Biotechnological, Environmental None Aquatic, Oil fields Oil tank USA 56.1 Public Gc00672 Gi01334 001746_GCAT 96561 18007 640196200 3944 3265 1 0 NC_009943 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished October 19, 2007 Richardson P microbes at cuba.jgi-psf.org
-Eukaryota Ascomycota Saccharomycetales Saccharomycetaceae Kluyveromyces Kluyveromyces waltii EUKARYAL Kluyveromyces waltii NCYC 2644 ABI 8x Genome FUNGI-ASCOMYCOTA Quality Draft complete Evolutionary, FGI None USA Public Gc00671 Gi00717 002033_GCAT 262981 10734 11000 5230 8 0 AADM010000000 NCBI Broad Institute Nature 428, 617-24 April 8, 2004 Kellis, M manoli at mit.edu
-Eukaryota Apicomplexa unclassified Babesiidae Babesia Babesia bovis EUKARYAL Babesia bovis T2Bo ABI 11x Genome PROTISTS-APICOMPLEXA Quality Draft complete USA 41.8 Public Gc00670 Gi02145 002797_GCAT 5865 18731 8200 3671 4 AAXT00000000 TIGR USDA PLoS Pathog 3, e148 October 19, 2007 Nene VM vnene at som.umaryland.edu
-Bacteria Proteobacteria Rhizobiales Xanthobacteraceae Azorhizobium Azorhizobium caulinodans BACTERIAL Azorhizobium caulinodans ORS 571 Sesbania rostrata Genome PROTEOBACTERIA-ALPHA Complete complete Nitrogen fixation, Mesophile Agricultural None Host Sesbania rostrata Japan Public Gc00669 Gi01986 002615_GCAT 438753 19267 5369 4717 1 0 NC_009937 NCBI Univ of Tokyo Unpublished October 17, 2007 Oyaizu H aoyaizu at mail.ecc.u-tokyo.ac.jp
-Eukaryota unclassified unclassified Hexamitidae Giardia Giardia intestinalis EUKARYAL Giardia lamblia (intestinalis) WB, clone C6 ABI ATCC 50803 Genome PROTISTS-DIPLOMONADIDA Quality Draft complete USA 49 Public Gc00668 Gi00274 001866_GCAT 184922 1439 640281002 11192 13100 5 0 NZ_AACB00000000 NCBI, MBL Marine Biological Laboratory NIH-NIAID Science 317, 1921-6 October 1, 2007 Sogin ML http://hermes.mbl.edu/labs/Sogin/Pages/PERSONNEL/Mitch.html
-Bacteria Cyanobacteria unclassified unclassified Acaryochloris Acaryochloris marina BACTERIAL Acaryochloris marina MBIC11017 ABI, 454 6x-ABI, 24x-454 Genome CYANOBACTERIA Complete complete Photosynthetic, Symbiont, Aerobe, Sphere-shaped, Mesophile, Mesophile Biotechnological None Marine Colonial ascidian from the Palau Islands USA Public Gc00667 Gi00728 000610_GCAT 329726 12997 6503 6254 1 9 NC_009925 NCBI, TGen Washington Univ, Arizona State Univ, TGen NSF Unpublished October 17, 2007 Blankenship RE Blankenship at asu.edu
-Bacteria Firmicutes Clostridiales Clostridiaceae Alkaliphilus Alkaliphilus oremlandii BACTERIAL Alkaliphilus (Clostridium) oremlandii OhILAs ABI, 454 12x Genome FIRMICUTES Complete incomplete Anaerobe, Nitrogen fixation, Sporulating, Rod-shaped, Motile, Sporulating, Non-Pathogen, Arsenic metabolizer, Mesophile Biotechnological, Environmental None Aquatic Ohio River sediment USA 36 Public Gc00666 Gi00933 000972_GCAT 350688 16083 638341068 2123 2836 1 0 NC_009922 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished October 11, 2007 Richardson P microbes at cuba.jgi-psf.org
-Eukaryota Streptophyta Vitales Vitaceae Vitis Vitis vinifera EUKARYAL Vitis vinifera PN40024 ABI 8.4x Genome PLANTS-STREPTOPHYTA Quality Draft incomplete France Public Gc00665 Gi01530 002312_GCAT 29760 18785 475000 CAAP00000000 NCBI, Genoscope Genoscope, INRA, Univ of Padua, Univ of Milan, Univ of Udine Nature 449, 463-7 September 27, 2007 Wincker P pwincker at genoscope.cns.fr
-Eukaryota Chlorophyta Chlamydomonadales Chlamydomonadaceae Chlamydomonas Chlamydomonas reinhardtii EUKARYAL Chlamydomonas reinhardtii CC-503 cw92 mt+ ABI 10x Genome PLANTS-CHLOROPHYTA Quality Draft incomplete Massachusetts in 1945 USA 65 Public Gc00664 Gi00816 002199_GCAT 3055 12260 100000 15256 17 0 ABCN00000000 NCBI, Joint Genome Institute, Chlamydomonas Center Joint Genome Institute DOE, NSF Science 318, 245-50 October 12, 2007 Grossman A arthur at andrew2.stanford.edu
-Bacteria Proteobacteria Alteromonadales Shewanellaceae Shewanella Shewanella halifaxensis BACTERIAL Shewanella pealeana ANG-SQ1 ABI 10x ATCC 700345 Genome PROTEOBACTERIA-GAMMA Complete complete Facultative, Psychrotolerant, Motile, Rod-shaped, Mesophile None Host Microbial community colonizing the accessory nidamental gland of the squid Loligo pealei USA 44 Public Gc00663 Gi01355 001772_GCAT 3055 17415 639857031 5174 4241 1 0 NC_009901 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished October 4, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Proteobacteria Rickettsiales Rickettsiaceae Rickettsia Rickettsia massiliae BACTERIAL Rickettsia massiliae MTU5 ATCC VR-1376 Genome PROTEOBACTERIA-ALPHA Complete complete Non-Pathogen, Aerobe, Nonmotile, Nonsporulating, Obligate parasite, Mesophile Medical None Host Rhipicephalus turanicus ticks collected near Marseille France France 32.5 Public Gc00662 Gi00812 001423_GCAT 416276 18271 1360 968 1 1 NC_009900 NCBI CNRS CNRG Unpublished October 4, 2007 Raoult D didier.raoult at medecine.univ-mrs.fr
-Bacteria Proteobacteria Rickettsiales Rickettsiaceae Rickettsia Rickettsia bellii BACTERIAL Rickettsia bellii OSU 85-389 ABI Dermacentor variabilis adult female tick Genome PROTEOBACTERIA-ALPHA Complete complete Pathogen, Aerobe, Nonmotile, Nonsporulating, Obligate parasite, Mesophile Medical, Human Pathogen Epidemic typhus Host Isolated in Vero cell culture at 34 C by Karl Poetter and Chip Pretzman; spaghetti forms seen USA 31.6 Public Gc00661 Gi01647 001420_GCAT 391896 17237 640753044 1528 1476 1 0 NC_009883 NCBI Univ of Iowa Unpublished October 2, 2007
-Bacteria Proteobacteria Rickettsiales Rickettsiaceae Rickettsia Rickettsia canadensis BACTERIAL Rickettsia canadensis McKiel ABI Tick Genome PROTEOBACTERIA-ALPHA Complete complete Pathogen, Aerobe, Nonmotile, Nonsporulating, Obligate parasite, Mesophile Medical, Human Pathogen Epidemic typhus Host Ticks in Canada USA 31 Public Gc00660 Gi01536 001421_GCAT 293613 12952 640753045 1159 1093 1 0 NC_009879 NCBI Univ of Iowa Unpublished October 1, 2007
-Bacteria Proteobacteria Rhodobacterales Rhodobacteraceae Dinoroseobacter Dinoroseobacter shibae BACTERIAL Dinoroseobacter shibae DFL-12 ABI 12x DSM 16493, NCIMB 14021 Genome PROTEOBACTERIA-ALPHA Complete complete Aerobe, Anoxygenic, Phototroph, Motile, Mesophile None Aquatic 33 Marine dinoflagellates from the Bay of Tokyo USA 65 Public Gc00659 Gi01335 001747_GCAT 398580 17417 639857026 3789 3577 1 5 NC_009952 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished October 5, 2007 Wagner-Dobler I Irene.Wagner-Doebler at helmholtz-hzi.de
-Bacteria Actinobacteria Actinomycetales Frankiaceae Frankia Frankia sp. EAN1pec BACTERIAL Frankia sp. Mbj2, EAN1pec ABI Plants Genome ACTINOBACTERIA Complete complete Aerobe, Mesophile, Chemoorganotroph, Nitrogen fixation, Non-Pathogen, Plant symbiont, Mesophile Biotechnological None Soil Kettering Research Laboratory in Ohio by M Lalonde in 1978 USA 70.9 Public Gc00658 Gi00260 001091_GCAT 298653 8982 638341096 9035 7191 1 0 NC_009921 NCBI, Joint Genome Institute, FrankiaGenomes Joint Genome Institute DOE Unpublished October 10, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Proteobacteria Campylobacterales Campylobacteraceae Arcobacter Arcobacter butzleri BACTERIAL Arcobacter butzleri RM4018 ABI Genome PROTEOBACTERIA-EPSILON Complete complete Pathogen, Aerobe, Motile, Nonsporulating, Spiral-shaped, Mesophile Medical, Human Pathogen Gastroenteritis, Bacteremia Host, Aquatic, Marine Human patient with gastroenteritis USA Public Gc00657 003099_GCAT 367737 16319 640753004 2341 2259 1 0 NC_009850 NCBI Agencourt Bioscience, ARS-USDA USDA Unpublished September 27, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacillus pumilus BACTERIAL Bacillus pumilus SAFR-032 Genome FIRMICUTES Complete complete Sporulating, Radiation resistant, Pathogen, Rod-shaped, Motile, Aerobe, Mesophile Medical None Soil Spacecraft Assembly Facility at NASA Jet Propulsion Laboratory USA Public Gc00656 Gi00716 000741_GCAT 315750 20391 3704 3681 1 0 NC_009848 NCBI, BCM-HGSC BCM-HGSC NSF PLoS ONE 2, e928 September 26, 2007 Weinstock G gwstock at bcm.tmc.edu
-Eukaryota Chordata Primates Hominidae Homo Homo sapiens EUKARYAL Homo sapiens JC Venter ABI 7.5x Genome CHORDATA-PRIMATES Quality Draft complete Caucasian, Male, Mesophile, Aerobe Medical 36 Sperm and white blood cells of a single Human individual USA Public Gc00655 Gi02160 002812_GCAT 9606 19621 2782357 24 0 ABBA01000000 NCBI, Ensembl J Craig Venter Institute PLoS Biology 5, e254 September 21, 2007 Levy S slevy at jcvi.org
-Eukaryota Ascomycota Hypocreales Nectriaceae Gibberella Gibberella zeae EUKARYAL Fusarium (Gibberella) graminearum (zeae) PH-1 ABI 10x NRRL 31084 Genome FUNGI-ASCOMYCOTA Quality Draft complete Pathogen, Mycotoxin producer, Mesophile Agricultural, Plant Pathogen, FGI Head blight USA Public Gc00654 Gi00263 002010_GCAT 229533 13839 640281006 36000 4 0 AACM02000000 NCBI, Broad Institute Broad Institute, IGGR NRI Science 317, 1400-2 September 7, 2007 Webmaster annotation-info at genome.wi.mit.edu
-Eukaryota Nematoda Spirurida Onchocercidae Brugia Brugia malayi EUKARYAL Brugia malayi NIAID/TRS ABI Genome NEMATODES Quality Draft complete Mesophile USA Public Gc00653 Gi00102 002123_GCAT 6279 10729 90000 11500 6 0 AAQA00000000 NCBI, TIGR, NematodeNet, TIGR TIGR, Univ of Pittsburgh NIH-NIAID Science 317, 1756 - 1760 September 21, 2007 Ghedin E GhedinE at dom.pitt.edu
-Bacteria Proteobacteria Campylobacterales Campylobacteraceae Campylobacter Campylobacter jejuni BACTERIAL Campylobacter jejuni jejuni 81116 ABI NCTC 11828 Genome PROTEOBACTERIA-EPSILON Complete complete Motile, Spiral-shaped, Pathogen, Food poisoning, Mesophile Medical, Human Pathogen Food poisoning Wastewater Waterborne outbreak in 1982 United Kingdom 30 Public Gc00652 Gi01671 000823_GCAT 407148 17953 640753013 1628 1626 1 0 NC_009839 NCBI BBSRC Institute of Food Research J. Bacteriology Epub September 20, 2007
-Bacteria Cyanobacteria Prochlorales Prochlorococcaceae Prochlorococcus Prochlorococcus marinus BACTERIAL Prochlorococcus marinus MIT 9215 ABI Genome CYANOBACTERIA Complete complete Nonmotile, Carbon cycle, Mesophile Environmental None Marine USA Public Gc00651 Gi01896 001369_GCAT 93060 18633 640753041 1738 1983 1 0 NC_009840 NCBI Joint Genome Institute DOE Unpublished September 20, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Chloroflexi Chloroflexales Chloroflexaceae Roseiflexus Roseiflexus castenholzii BACTERIAL Roseiflexus castenholzii HLO8, DSM 13941 ABI 10x DSM 13941 Genome CHLOROFLEXI Complete complete Filament-shaped, Photosynthetic, Thermophile, Facultative, Motile, Photoautotroph Biotechnological None Marine, Hot spring 50 Hot spring microbial mat USA 60.7 Public Gc00650 Gi00962 001429_GCAT 120962 13462 640753047 5723 4330 1 0 NC_009767 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished August 13, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Thermotogae Thermotogales Thermotogaceae Thermotoga Thermotoga lettingae BACTERIAL Thermotoga lettingae TMOT ABI Genome THERMOTOGAE Complete complete Rod-shaped, Thermophile, Anaerobe, Heterotroph, Motile, Nonsporulating, Methanol degrading Evolutionary, Biotechnological None Aquatic 65 Methanol-degrading, sulfate-reducing bioreactor USA 38.7 Public Gc00649 Gi01044 001609_GCAT 416591 15644 2135 2040 1 0 NC_009828 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished September 18, 2007 Richardson P microbes at cuba.jgi-psf.org
-Eukaryota Ascomycota Saccharomycetales Saccharomycetaceae Vanderwaltozyma Vanderwaltozyma polyspora EUKARYAL Vanderwaltozyma polyspora DSM 70294 ABI 7.8x DSM 70294 Genome FUNGI-ASCOMYCOTA Quality Draft complete Mesophile Evolutionary Ireland 33 Public Gc00648 Gi02041 002688_GCAT 436907 19237 14661 5367 NZ_AAZN00000000 NCBI Trinity College PNAS 104, 8397-8402 August 17, 2007 Wolfe KH http://wolfe.gen.tcd.ie/
-Bacteria Proteobacteria Enterobacteriales Enterobacteriaceae Serratia Serratia proteamaculans BACTERIAL Serratia proteamaculans 568 ABI 11.7x Genome PROTEOBACTERIA-GAMMA Complete complete Facultative, Motile, Rod-shaped, Aerobe, Pathogen, Mesophile Medical, Human Pathogen, Environmental, Bioremediation Pneumonia Host, Soil USA 55 Public Gc00647 Gi01353 001770_GCAT 399741 17459 640753048 5448 4891 1 1 NC_009832 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished September 18, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Proteobacteria Alteromonadales Shewanellaceae Shewanella Shewanella sediminis BACTERIAL Shewanella sediminis HAW-EB3T ABI NCIMB 14036, DSM 17055 Genome PROTEOBACTERIA-GAMMA Complete complete Facultative, Psychrophile, Motile, Rod-shaped, Nonsporulating Biotechnological, Degrades RDX None Marine 10 Sediment at depth of 215m from an unexploded-ordinance-dumping site at Halifax USA 46 Public Gc00646 Gi01356 001773_GCAT 425104 18789 640753050 5517 4497 1 0 NC_009831 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished September 18, 2007 Richardson P microbes at cuba.jgi-psf.org
-Eukaryota Cnidaria Actiniaria Edwardsiidae Nematostella Nematostella vectensis EUKARYAL Nematostella vectensis CH2 x CH6 ABI 7.8x Genome CNIDARIA Quality Draft complete Mesophile Model organism USA 40.6 Public Gc00645 Gi00773 002244_GCAT 45351 12581 297398 NZ_ABAV00000000 NCBI, Joint Genome Institute Joint Genome Institute DOE Science 317, 86-94 August 22, 2007 Rokhsar D http://mcb.berkeley.edu/faculty/GEN/rokhsard.html
-Bacteria Proteobacteria Campylobacterales Campylobacteraceae Campylobacter Campylobacter concisus BACTERIAL Campylobacter concisus 13826 ABI Genome PROTEOBACTERIA-EPSILON Complete complete Motile, Spiral-shaped, Pathogen, Food poisoning, Nonsporulating, Mesophile Medical, Human Pathogen Gingivitis, Periodontitis, Periodontosis, Gastroenteritis Host, Wastewater Feces of a patient with bloody diarrhea in Denmark USA 39.3 Public Gc00644 Gi01266 000829_GCAT 360104 17159 640753009 2052 1929 1 2 NC_009802 NCBI, TIGR TIGR NIH-NIAID Unpublished September 12, 2007 Nelson KE http://www.tigr.org/~kenelson/
-Bacteria Firmicutes Lactobacillales Streptococcaceae Streptococcus Streptococcus gordonii BACTERIAL Streptococcus gordonii Challis CH1 ATCC 35105, NCTC7868 Genome FIRMICUTES Complete complete Pathogen, Nonmotile, Nonsporulating, Facultative, Coccus-shaped, Mesophile Medical, Human Pathogen Dental plaque, Endocarditis, Periodontal infection Human oral microflora, Host 37 USA 42 Public Gc00643 Gi00608 001537_GCAT 467705 66 640753055 2196 2051 1 0 NC_009785 NCBI TIGR NIH-NIDCR Unpublished September 11, 2007 Gill SR srgill at tigr.org
-Bacteria Proteobacteria Enterobacteriales Enterobacteriaceae Citrobacter Citrobacter koseri BACTERIAL Citrobacter koseri CDC 4225-83 ABI 8x ATCC BAA-895, SGSC4696 Genome PROTEOBACTERIA-GAMMA Complete incomplete Facultative, Motile, Pathogen, Mesophile Medical, Human Pathogen, Animal Pathogen Bacteremia, Meningoencephalitis, Neonatal meningitis, Brain abscesses Soil, Aquatic, Food, Intestinal microflora, Host 1983 in Maryland where it caused neonatal meningitis USA Public Gc00642 Gi00708 000962_GCAT 290338 12716 640753015 4720 5003 1 2 NC_009792 NCBI, Washington Univ Washington Univ NIH-NIAID Unpublished September 11, 2007 Clifton S sclifton at watson.wustl.edu
-Bacteria Proteobacteria Enterobacteriales Enterobacteriaceae Escherichia Escherichia coli BACTERIAL Escherichia coli O139:H28 E24377A (ETEC) O139:H28 ABI Genome PROTEOBACTERIA-GAMMA complete complete Pathogen, Enterotoxigenic, Rod-shaped, Motile, Facultative, Nonsporulating, Mesophile Medical, Human Pathogen Diarrhea Host, Human intestinal microflora 37 USA 50 Public Gc00641 Gi00940 001030_GCAT 331111 13960 640753024 4979 4755 1 6 NC_009801 NCBI TIGR Unpublished September 11, 2007 Ravel J http://www.tigr.org/faculty/Ravel_Jacques/index.shtml
-Bacteria Proteobacteria Enterobacteriales Enterobacteriaceae Escherichia Escherichia coli BACTERIAL Escherichia coli O9 HS O9 ABI Genome PROTEOBACTERIA-GAMMA complete complete Rod-shaped, Motile, Facultative, Pathogen, Nonsporulating, Mesophile Medical, Human Pathogen Diarrhea Host, Human intestinal microflora Walter Reed Army Institute of Research in 1978 USA 50 Public Gc00640 Gi01140 001037_GCAT 331112 13959 640753025 4643 4384 1 0 NC_009800 NCBI TIGR NIH-NIAID Unpublished September 10, 2007 Ravel J http://www.tigr.org/faculty/Ravel_Jacques/index.shtml
-Bacteria Firmicutes Bacillales Staphylococcaceae Staphylococcus Staphylococcus aureus BACTERIAL Staphylococcus aureus aureus Mu3 Genome FIRMICUTES complete complete Pathogen, Nonmotile, Facultative, Coccus-shaped, Nonsporulating, Mesophile Medical, Human Pathogen, Animal Pathogen, Cattle Pathogen, Poultry Pathogen Mastitis, Nosocomial infection Host 30 - 37 Japan Public Gc00639 003050_GCAT 418127 18509 640753053 2880 2698 1 0 NC_009782 NCBI, Juntendo Univ Juntendo Univ Unpublished September 4, 2007 Hiramatsu K khiram06 at med.juntendo.ac.jp
-Bacteria Proteobacteria Enterobacteriales Enterobacteriaceae Cronobacter Enterobacter sakazakii BACTERIAL Enterobacter sakazakii ATCC BAA-894 ABI 8x ATCC BAA-894 Genome PROTEOBACTERIA-GAMMA complete complete Facultative, Pathogen, Rod-shaped, Motile, Anaerobe, Mesophile Medical, Human Pathogen Meningitis, Septicemia, Necrotizing enterocolitis Host 37 Powdered milk formula fed to a hospitalized neonate that developed an infection USA 87 Public Gc00638 Gi00537 001451_GCAT 290339 12720 640753022 4368 4277 1 2 NC_009778 NCBI, Washington Univ Washington Univ NIH-NIAID Unpublished August 28, 2007 Clifton S sclifton at watson.wustl.edu
-Bacteria Proteobacteria Vibrionales Vibrionaceae Vibrio Vibrio harveyi BACTERIAL Vibrio harveyi BB120, ATCC BAA-1116 ABI, 454 10.8x ATCC BAA-1116 Genome PROTEOBACTERIA-GAMMA complete complete Bioluminescent, Rod-shaped, Motile, Facultative, Mesophile Environmental None Marine 20 - 30 Ocean isolate obtained in 1993 USA 85 Public Gc00637 Gi01254 001691_GCAT 669 19857 5969 5944 2 1 NC_009783, NC_009784 NCBI, Washington Univ Princeton Univ, Washington Univ NSF Unpublished August 28, 2007 Bassler B http://www.molbio.princeton.edu/research_facultymember.php?id=5
-Archaea Crenarchaeota Desulfurococcales Desulfurococcaceae Ignicoccus Ignicoccus hospitalis ARCHAEAL Ignicoccus hospitalis Kin4/I ABI 12x DSM 18386 Nanoarchaeum equitans Genome CRENARCHAEOTA-THERMOPROTEI complete complete Hyperthermophile, Chemolithoautotroph, Coccus-shaped, Nonsporulating, Motile, Anaerobe Biotechnological None Marine, Hydrothermal vent Shallow marine hydrothermal system of the Kolbeinsey Ridge, north of Iceland USA 61.2 Public Gc00636 Gi01875 001809_GCAT 453591 13914 640062401 1297 1434 1 0 NC_009776 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished August 29, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Proteobacteria Thiotrichales Francisellaceae Francisella Francisella tularensis BACTERIAL Francisella tularensis holarctica FTA ABI Genome PROTEOBACTERIA-GAMMA complete complete Pathogen, Nonmotile, Aerobe, Coccus-shaped, Nonsporulating, Mesophile Medical, Human Pathogen, Biothreat Tularemia Host, Aquatic Patient with type B tularemia USA 32 Public Gc00635 Gi02287 003009_GCAT 458234 20197 640753028 1890 2079 1 0 NC_009749 NCBI Joint Genome Institute, Los Alamos National Laboratory, BioHealthBase Unpublished August 23, 2007 Brettin T brettin at lanl.gov
-unclassified unclassified unclassified unclassified unclassified unclassified BACTERIAL Coxiella burnetii Dugway 7E9-12 ABI Genome PROTEOBACTERIA-GAMMA complete complete Pathogen, Facultative, Motile, Mesophile Medical, Human Pathogen, Biothreat, Animal Pathogen Q fever, Food poisoning Host Rodents in Utah USA 42 Public Gc00634 Gi01269 000983_GCAT 382253 16721 640753021 2158 2058 1 1 NC_009727 NCBI, TIGR TIGR NIH-NIAID Unpublished August 1, 2007 Samuel JE jsamuel at medicine.tamhsc.edu
-Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacillus amyloliquefaciens BACTERIAL Bacillus amyloliquefaciens FZB42 Genome FIRMICUTES complete complete Rhizosphere-colonizing, Rod-shaped, Sporulating, Aerobe, Mesophile Biotechnological, Antibiotic production, Suppresses Plant Pathogens, Agricultural None Soil Soil Germany 46 Public Gc00633 Gi00049 000711_GCAT 326423 13403 640753005 3918 3693 1 0 NC_009725 NCBI, Goettingen Genomics Laboratory Competence Network, Goettingen Genomics Laboratory Nature Biotechnol 25, 1007-14 August 1, 2007 Borriss R rainer.borriss at rz.hu-berlin.de
-Bacteria Proteobacteria Rhizobiales Xanthobacteraceae Xanthobacter Xanthobacter autotrophicus BACTERIAL Xanthobacter autotrophicus Py2 ABI 12x ATCC 35674, DSM 432 Genome PROTEOBACTERIA-ALPHA complete complete Nitrogen fixation, Rod-shaped, Facultative, Motile, Mesophile Environmental, Bioremediation None Soil, Aquatic, Sediment USA 67 Public Gc00632 Gi00972 001697_GCAT 78245 15756 640753059 5308 4746 1 1 NC_009720 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished July 30, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Proteobacteria Rhizobiales Phyllobacteriaceae Parvibaculum Parvibaculum lavamentivorans BACTERIAL Parvibaculum lavamentivorans DS-1 ABI 17.5x DSM 13023, NCIMB 13966 Genome PROTEOBACTERIA-ALPHA complete complete Heterotroph, Rod-shaped, Aerobe, Motile, Surfactant-degrading, Mesophile Biotechnological, Bioremediation None Sludge 30 Sewage treatment plant in Germany USA 62 Public Gc00631 Gi01347 001764_GCAT 402881 17639 640753040 3914 3636 1 0 NC_009719 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished July 30, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Thermotogae Thermotogales Thermotogaceae Fervidobacterium Fervidobacterium nodosum BACTERIAL Fervidobacterium nodosum Rt17-B1 ABI 11.5x Genome THERMOTOGAE Complete complete Rod-shaped, Thermophile, Anaerobe, Chemoorganotroph, Motile, Nonsporulating Evolutionary, Biotechnological None Aquatic, Hot spring 70 Hot spring in New Zealand USA 34 Public Gc00630 Gi01012 001054_GCAT 381764 16719 640753026 1948 1750 1 0 NC_009718 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished July 30, 2007 Richardson P microbes at cuba.jgi-psf.org
-Archaea Euryarchaeota Methanomicrobiales unclassified Candidatus Methanoregula Candidatus Methanoregula boonei ARCHAEAL Candidatus Methanoregula boonei 6A8 ABI Genome EURYARCHAEOTA-METHANOMICROBIA Complete complete Methanogen, Acidophile, Anaerobe, Rod-shaped, Mesophile, Lithotroph Biotechnological, Energy production None Aquatic 4-6 37 Acidic peat bog in New York State USA 54 Public Gc00629 Gi01473 001806_GCAT 456442 18505 640753014 2542 2450 1 0 NC_009712 NCBI, Joint Genome Institute Joint Genome Institute DOE Unpublished July 26, 2007 Richardson P microbes at cuba.jgi-psf.org
-Bacteria Proteobacteria Campylobacterales Campylobacteraceae Campylobacter Campylobacter curvus BACTERIAL Campylobacter curvus 525.92 ABI Genome PROTEOBACTERIA-EPSILON Complete complete Motile, Spiral-shaped, Pathogen, Food poisoning, Mesophile Medical, Human Pathogen Gastroenteritis, Periodontal infection Host, Wastewater Feces of a patient with diarrhea in South Africa USA 44 Public Gc00628 Gi01267 000830_GCAT 360105 17161 640753010 1971 1931 1 0 NC_009715 NCBI, TIGR J Craig Venter Institute NIH-NIAID Unpublished July 25, 2007 Nelson K http://www.tigr.org/~kenelson/
-Bacteria Proteobacteria Campylobacterales Campylobacteraceae Campylobacter Campylobacter hominis BACTERIAL Campylobacter hominis ATCC BAA-381 ABI ATCC BAA-381, NCTC 13146T, LMG 19568T Genome PROTEOBACTERIA-EPSILON Complete complete Nonmotile, Rod-shaped, Non-Pathogen, Nonsporulating, Mesophile Medical None Host, Gastrointestinal tract 37 Feces of a healthy human in 2001 USA 31 Public Gc00627 Gi01268 000831_GCAT 360107 20083 640753011 1711 1682 1 1 NC_009714 NCBI, TIGR J Craig Venter Institute NIH-NIAID Unpublished July 25, 2007 Nelson K http://www.tigr.org/~kenelson/
[TRUNCATED]
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svnlook diff /svnroot/seqinr -r 1828
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