Bacillus anthracis

Background

• 89 known strains
• Most virulent: Ames(USA 2001), Vollum (WWII, biological weapon)
• Benign: Sterne (used as vaccine)

• Ames, AmesAncestor, Stern are 99.9% identical; no rearrangements

Genome Projects

NIH Genome Projects

 Center          Complete     Assembly    Progress  Total
 TIGR/JCVI       2            8           1         11
 LANL            0            6           0         6
 DOE             1            0           0         1 
 NMRC            0            0           2         2
 Total           3            14          3         20

TIGR/JCVI Strains

 Contigs  Traces   Status    Completed   Strain 
 0        96,532   Progress  .           A0039  
 62       67,600   Assembly  2007/07/25  Tsiankovskii-I AA ; ??? possible update
 1(+2)    101,379  Complete  2004/05/20  Ames Ancestor (Ames 0581)  AA ; Insignia
 42       86,181   Assembly  2004/06/04  A1055 AA ; Insignia
 1(+2)    83,552   Assembly  2005/05/16  A2012 ??? not in Insignia
 1        125,879  Complete  2002/05/16  Ames  ??? complete but not in AA ; Insignia
 49       0        Assembly  2004/06/07  Australia 94   ??? no TRACES ; Insignia
 30       90,308   Assembly  2004/06/04  CNEVA-9066 Insignia
 64       92,429   Assembly  2004/06/07  Kruger B AA ; Insignia
 52       103,144  Assembly  2004/06/04  Vollum Insignia
 44       95,078   Assembly  2004/06/07  Western North America USA6153 Insignia

LANL Strains

No traces in TA; none in Insignia

 Contigs  Traces   Status    Completed    Strain       
 60       0        Assembly  2008/04/08   A0174
 60       0        Assembly  2008/02/12   A0193                              
 68       0        Assembly  2008/03/24   A0389
 46       0        Assembly  2008/02/12   A0442
 57       0        Assembly  2008/03/24   A0465
 63       0        Assembly  2008/01/16   A0488

+ 2 plasmid genome projects (pX01,pX02) completed in 1999

DOE Strains

 Contigs  Traces   Status    Completed    Strain
 1        147,665  Complete  2004/06/24   Sterne ??? complete but not in AA; Insignia

Naval Medical Research Center

 Contigs  Traces   Status    Strain
 0        0        Progress  34F2(NMRC)
 0        0        Progress  34F2 delta gerH

Ames

• not in AA
• assembly recreated with "AMOScmp-alignmentTrimmed -D LAYERR=90" => 1 piece
• Many stretched & missoriented mates
• Location: /fs/szasmg3/dpuiu/Bacilus_anthracis/Ames/Assembly/2008_0820_AMOScmp-alignmentTrimmed

Ames Ancestor

• Complete & in AA
• Downloaded from AA and converted to bank
• Location: /fs/szasmg3/dpuiu/Bacilus_anthracis/AmesAncestor/CS--AI-293

Sterne

Complete but not in AA. Tried to reassemble it at CBCB

AMOScmp

• version: June 12 2007
• untrimmed reads => 358 ctg
• 53 zero cvg regions, max is almost 5K

CA

• runCA-OBT.pl script
• version 5.1
• Output:

 ctg        204
 deg        145
 scf        186
 singleton  2418