Difference between revisions of "Francisella tularensis"

From Cbcb
Jump to navigation Jump to search
Line 80: Line 80:
 
* ~dpuiu/Data/F_tularensis/
 
* ~dpuiu/Data/F_tularensis/
 
* /fs/szasmg/Bacteria/F_tularensis
 
* /fs/szasmg/Bacteria/F_tularensis
 
== 454 ==
 
Paired End reads:
 
  * approximately 84-nucleotide DNA fragments
 
  * have a 44-mer adaptor sequence in the middle
 
  * flanked by a 20-mer sequence on each side.
 
  * The two flanking 20-mers are segments of DNA that were originally located approximately 2.5 kb apart in the genome of interest. 
 
  * The ordering and orienting of contigs generates scaffolds which provide a high-quality draft sequence of the genome.
 
  [http://www.454.com/downloads/protocols/1_paired_end.pdf pair read article]
 

Revision as of 14:50, 17 October 2007

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
  • FSC198 Univ. of Birmingham , Complete ( 1,892,616 bp) NC_008245
  • WY96-3418 BioHealthBase , Complete (1,898,476 bp) NC_009257
  • FSC033 Broad, Assembly (15 contigs) ***
  • ATCC6223 Baylor (88 contigs) ***

Type B

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

Novicida

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

Mediasiatica

File Locations on Disk

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