Francisella tularensis: Difference between revisions

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== Data Sources ==
= Characteristics =
 
* gamma—proteobacterium
* one of the most infectious human intracellular pathogens
* causative agent of tularemia
* category A biodefense concern because of its ability to cause incapacitating, potentially fatal illness
 
'''4 subspecies: tularensis, holarctica, novicida, mediasiatica'''
 
  Subspecies         Virulence Region
  tularensis (Type A) high         North America,
  holarctica (Type B) moderate        North America,Europe, Asia
  novicida              moderate        .
  mediasiatica         low         .
 
= Data Sources =


NCBI:
NCBI:


* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=francisella%20tularensis  Genome Projects]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=francisella%20tularensis  Genome Projects]
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/BCM/ SRA BCM]
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/ SRA]
* [http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&size=310747&val=species_code%3D%22Francisella+tularensis%22+&file=trace&gz=on&fasta=on&dopt=fasta&dispmax=5&page=1  TA]
* [http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&size=310747&val=species_code%3D%22Francisella+tularensis%22+&file=trace&gz=on&fasta=on&dopt=fasta&dispmax=5&page=1  TA]
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/francisella_tularensis TA FTP]
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/francisella_tularensis TA FTP]
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* [http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonList&page=lineageMicrobes&genus=Francisella Comparative analysis]
* [http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonList&page=lineageMicrobes&genus=Francisella Comparative analysis]


== Read Counts ==
Univ. of Washington:
* [http://www.genome.washington.edu/UWGC/Projects/index.cfm?PID=184&ST=4 Univ. of Washington Genome Center]
 
= Read Counts =


* [[Media:Francisella_tularensis.pdf|Francisella_tularensis.pdf]]
* [[Media:Francisella_tularensis.pdf|Francisella_tularensis.pdf]]
* [[Media:Francisella_tularensis.sxc|Francisella_tularensis.sxc]]
* [[Media:Francisella_tularensis.sxc|Francisella_tularensis.sxc]]
* [[Media:Francisella_tularensis.ppt|Francisella_tularensis.ppt]]


== Type A ==
= Type A =
* [[Francisella_tularensis_tularensis_SCHU_S4|SCHU_S4]] SDRA , Complete (1,892,819 bp) NC_006570
* [[Francisella_tularensis_tularensis_SCHU_S4|SCHU_S4]] SDRA , Complete (1,892,819 bp) NC_006570 ; uploaded to Insignia
* [[Francisella_tularensis_tularensis_FSC198|FSC198]] Univ. of Birmingham , Complete ( 1,892,616 bp) NC_008245
* [[Francisella_tularensis_tularensis_FSC198|FSC198]] Univ. of Birmingham , Complete ( 1,892,616 bp) NC_008245 ; uploaded to Insignia
* [[Francisella_tularensis_tularensis_WY96-3418|WY96-3418]] BioHealthBase , Complete (1,898,476 bp) NC_009257
* [[Francisella_tularensis_tularensis_WY96-3418|WY96-3418]] BioHealthBase , Complete (1,898,476 bp) NC_009257 ; uploaded to Insignia
* [[Francisella_tularensis_tularensis_FSC033|FSC033]] Broad, Assembly (15 contigs) ***
* [[Francisella_tularensis_tularensis_FSC033|FSC033]] Broad, Assembly (15 contigs) *** ; uploaded to Insignia
* [[Francisella_tularensis_tularensis_ATCC6223|ATCC6223]] Baylor (88 contigs) ***
* [[Francisella_tularensis_tularensis_ATCC6223|ATCC6223]] Baylor (88 contigs) ***


== Type B ==
= Type B =


* [[Francisella_tularensis_holarctica_LVS|LVS]] LLNL, Complete (1,895,994 bp) NC_007880
* [[Francisella_tularensis_holarctica_LVS|LVS]] LLNL, Complete (1,895,994 bp) NC_007880 ; uploaded to Insignia
* [[Francisella_tularensis_holarctica_OSU18|OSU18]] Baylor, Complete (1,895,727 bp) NC_008369 ***
* [[Francisella_tularensis_holarctica_OSU18|OSU18]] Baylor, Complete (1,895,727 bp) NC_008369 *** ; uploaded to Insignia
* [[Francisella_tularensis_holarctica_KO97|KO97]] Baylor (126 contigs) ***
* [[Francisella_tularensis_holarctica_KO97|KO97]] Baylor (126 contigs) ***
* [[Francisella_tularensis_holarctica_MI001730|MI001730]] Baylor (118 contigs) ***
* [[Francisella_tularensis_holarctica_MI001730|MI001730]] Baylor (118 contigs) ***
* [[Francisella_tularensis_holarctica_OR960246|OR960246]] Baylor (111 contigs) ***
* [[Francisella_tularensis_holarctica_OR960246|OR960246]] Baylor (111 contigs) ***
* [[Francisella_tularensis_holarctica_RC503|RC503]] Baylor (115 contigs)
* [[Francisella_tularensis_holarctica_RC503|RC503]] Baylor (115 contigs)
* [[Francisella_tularensis_holarctica_275|275]] Broad (31 contigs) ***
* [[Francisella_tularensis_holarctica_257|257]] Broad (31 contigs) NZ_AAUD00000000 *** ; uploaded to Insignia
* [[Francisella_tularensis_holarctica_FSC022|FSC022]] Broad (19 contigs) ***
* [[Francisella_tularensis_holarctica_FSC022|FSC022]] Broad (19 contigs) NZ_AAYD00000000 *** ; uploaded to Insignia
* [[Francisella_tularensis_holarctica_FSC200|FSC200]] Univ of Washington (39 contigs) NZ_AASP00000000 ; uploaded to Insignia
* [[Francisella_tularensis_holarctica_FTA|FTA]] BioHealthBase/JGI/LANL, Progress ; uploaded to Insignia
* [[Francisella_tularensis_holarctica_URFT1|URFT1]] Unite des Rickettsies/CNRS, Progress


== Novicida ==
= Novicida =
* [[Francisella_tularensis_novicida_U112|U112]] Univ. of Washington, Complete (1,910,031 bp) NC_008601
* [[Francisella_tularensis_novicida_U112|U112]] Univ. of Washington, Complete (1,910,031 bp) NC_008601 ; uploaded to Insignia
* [[Francisella_tularensis_novicida_GA99-3548|GA99-3548]] Broad (18 contigs) ***  
* [[Francisella_tularensis_novicida_GA99-3548|GA99-3548]] Broad (18 contigs) NZ_ABAH00000000 *** ; uploaded to Insignia
* [[Francisella_tularensis_novicida_GA99-3549|GA99-3549]] Broad (15 contigs) ***
* [[Francisella_tularensis_novicida_GA99-3549|GA99-3549]] Broad (15 contigs) NZ_AAYF00000000 *** ; uploaded to Insignia


== Mediasiatica ==
= Mediasiatica =
* [[Francisella_tularensis_mediasiatica_FSC147|FSC147]] DOE, Progress


No traces available
= File Locations on Disk =
 
== File Locations on Disk ==


* /fs/szdata//ncbi/genomes/Bacteria/Francisella_tularensis
* /fs/szdata//ncbi/genomes/Bacteria/Francisella_tularensis
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* /fs/szasmg/Bacteria/F_tularensis
* /fs/szasmg/Bacteria/F_tularensis


== 454 ==
= Insignia uploads=
Paired End reads:
 
  * approximately 84-nucleotide DNA fragments
Assemblies selected:
  * have a 44-mer adaptor sequence in the middle
    /fs/szasmg2/Bacteria/F_tularensis_holarctica_FSC022/best
  * flanked by a 20-mer sequence on each side.
    /fs/szasmg2/Bacteria/F_tularensis_holarctica_KO97/best
  * The two flanking 20-mers are segments of DNA that were originally located approximately 2.5 kb apart in the genome of interest. 
    /fs/szasmg2/Bacteria/F_tularensis_holarctica_MI001730/best
  * The ordering and orienting of contigs generates scaffolds which provide a high-quality draft sequence of the genome.
    /fs/szasmg2/Bacteria/F_tularensis_holarctica_OR960246/best
  [http://www.454.com/downloads/protocols/1_paired_end.pdf pair read article]
    /fs/szasmg2/Bacteria/F_tularensis_holarctica_OSU18/best
    /fs/szasmg2/Bacteria/F_tularensis_holarctica_RC503/best
    /fs/szasmg2/Bacteria/F_tularensis_novicida_GA99-3548/best
    /fs/szasmg2/Bacteria/F_tularensis_novicida_GA99-3549/best
    /fs/szasmg2/Bacteria/F_tularensis_tularensis_257/best
    /fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/best
    /fs/szasmg2/Bacteria/F_tularensis_tularensis_FSC033/best

Latest revision as of 17:07, 8 December 2008

Characteristics

  • gamma—proteobacterium
  • one of the most infectious human intracellular pathogens
  • causative agent of tularemia
  • category A biodefense concern because of its ability to cause incapacitating, potentially fatal illness

4 subspecies: tularensis, holarctica, novicida, mediasiatica 

 Subspecies	        Virulence	Region
 tularensis (Type A)	high	        North America,
 holarctica (Type B)	moderate        North America,Europe, Asia
 novicida               moderate        .
 mediasiatica	        low	        .

Data Sources

NCBI:

Broad:

Baylor:

JGI:

Univ. of Washington:

Read Counts

Type A

  • SCHU_S4 SDRA , Complete (1,892,819 bp) NC_006570 ; uploaded to Insignia
  • FSC198 Univ. of Birmingham , Complete ( 1,892,616 bp) NC_008245 ; uploaded to Insignia
  • WY96-3418 BioHealthBase , Complete (1,898,476 bp) NC_009257 ; uploaded to Insignia
  • FSC033 Broad, Assembly (15 contigs) *** ; uploaded to Insignia
  • ATCC6223 Baylor (88 contigs) ***

Type B

  • LVS LLNL, Complete (1,895,994 bp) NC_007880 ; uploaded to Insignia
  • OSU18 Baylor, Complete (1,895,727 bp) NC_008369 *** ; uploaded to Insignia
  • KO97 Baylor (126 contigs) ***
  • MI001730 Baylor (118 contigs) ***
  • OR960246 Baylor (111 contigs) ***
  • RC503 Baylor (115 contigs)
  • 257 Broad (31 contigs) NZ_AAUD00000000 *** ; uploaded to Insignia
  • FSC022 Broad (19 contigs) NZ_AAYD00000000 *** ; uploaded to Insignia
  • FSC200 Univ of Washington (39 contigs) NZ_AASP00000000 ; uploaded to Insignia
  • FTA BioHealthBase/JGI/LANL, Progress ; uploaded to Insignia
  • URFT1 Unite des Rickettsies/CNRS, Progress

Novicida

  • U112 Univ. of Washington, Complete (1,910,031 bp) NC_008601 ; uploaded to Insignia
  • GA99-3548 Broad (18 contigs) NZ_ABAH00000000 *** ; uploaded to Insignia
  • GA99-3549 Broad (15 contigs) NZ_AAYF00000000 *** ; uploaded to Insignia

Mediasiatica

File Locations on Disk

  • /fs/szdata//ncbi/genomes/Bacteria/Francisella_tularensis
  • ~dpuiu/Data/F_tularensis/
  • /fs/szasmg/Bacteria/F_tularensis

Insignia uploads

Assemblies selected: 

   /fs/szasmg2/Bacteria/F_tularensis_holarctica_FSC022/best
   /fs/szasmg2/Bacteria/F_tularensis_holarctica_KO97/best
   /fs/szasmg2/Bacteria/F_tularensis_holarctica_MI001730/best
   /fs/szasmg2/Bacteria/F_tularensis_holarctica_OR960246/best
   /fs/szasmg2/Bacteria/F_tularensis_holarctica_OSU18/best
   /fs/szasmg2/Bacteria/F_tularensis_holarctica_RC503/best
   /fs/szasmg2/Bacteria/F_tularensis_novicida_GA99-3548/best
   /fs/szasmg2/Bacteria/F_tularensis_novicida_GA99-3549/best
   /fs/szasmg2/Bacteria/F_tularensis_tularensis_257/best
   /fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/best
   /fs/szasmg2/Bacteria/F_tularensis_tularensis_FSC033/best
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