Francisella tularensis: Difference between revisions

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== Characteristics ==
= Characteristics =


* gamma—proteobacterium
* gamma—proteobacterium
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'''4 subspecies: tularensis, holarctica, novicida, mediasiatica'''  
'''4 subspecies: tularensis, holarctica, novicida, mediasiatica'''  


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


== Data Sources ==
= 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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