Francisella tularensis: Difference between revisions

From Cbcb
Jump to navigation Jump to search
No edit summary
 
Line 1: Line 1:
== Characteristics ==
= Characteristics =


* gamma—proteobacterium
* gamma—proteobacterium
Line 14: Line 14:
   mediasiatica         low         .
   mediasiatica         low         .


== Data Sources ==
= Data Sources =


NCBI:
NCBI:
Line 40: Line 40:
* [http://www.genome.washington.edu/UWGC/Projects/index.cfm?PID=184&ST=4 Univ. of Washington Genome Center]
* [http://www.genome.washington.edu/UWGC/Projects/index.cfm?PID=184&ST=4 Univ. of Washington Genome Center]


== Read Counts ==
= Read Counts =


* [[Media:Francisella_tularensis.pdf|Francisella_tularensis.pdf]]
* [[Media:Francisella_tularensis.pdf|Francisella_tularensis.pdf]]
Line 46: Line 46:
* [[Media:Francisella_tularensis.ppt|Francisella_tularensis.ppt]]
* [[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 ; uploaded to Insignia
* [[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 ; uploaded to Insignia
* [[Francisella_tularensis_tularensis_FSC198|FSC198]] Univ. of Birmingham , Complete ( 1,892,616 bp) NC_008245 ; uploaded to Insignia
Line 53: Line 53:
* [[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 ; uploaded to Insignia
* [[Francisella_tularensis_holarctica_LVS|LVS]] LLNL, Complete (1,895,994 bp) NC_007880 ; uploaded to Insignia
Line 67: Line 67:
* [[Francisella_tularensis_holarctica_URFT1|URFT1]] Unite des Rickettsies/CNRS, Progress
* [[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 ; uploaded to Insignia
* [[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) NZ_ABAH00000000 *** ; uploaded to Insignia
* [[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) NZ_AAYF00000000 *** ; uploaded to Insignia
* [[Francisella_tularensis_novicida_GA99-3549|GA99-3549]] Broad (15 contigs) NZ_AAYF00000000 *** ; uploaded to Insignia


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


== File Locations on Disk ==
= File Locations on Disk =


* /fs/szdata//ncbi/genomes/Bacteria/Francisella_tularensis
* /fs/szdata//ncbi/genomes/Bacteria/Francisella_tularensis
Line 81: Line 81:
* /fs/szasmg/Bacteria/F_tularensis
* /fs/szasmg/Bacteria/F_tularensis


== Insignia uploads==
= Insignia uploads=


Assemblies selected:
Assemblies selected:

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