Clostridium botulinum other strains

!!! OLD; should be deleted

Other than the Sanger sequenced Hall strain A (ATCC 3502)

Summary:

 ~ 20 strains in NCBI Taxonomy
 9 genome projects
 8 complete genomes
 3 assemblies in NCBI AA (all TIGR/JCVI)
 6 trace sets (5 TIGR/JCVI , 1 Sanger)

Data sources

NCBI:

• Tax Browser
• Genome Projects
• NCBI_TA_FTP

Genome projects:

 1. A str. ATCC 19397 [LANL/JCVI/DOE] complete ; uploaded to Insignia
 2*: A str. ATCC 3502 [Sanger] complete ; uploaded to Insignia
 3: A str. Hall [LANL/JCVI/DOE] complete ; uploaded to Insignia
 4: Bf [JCVI/MSC] 70 contigs ; in AA
 5: C str. Eklund [JCVI/MSC] 76 contigs  ; in AA
 6: F str. Langeland plasmid pCLI [LANL/JCVI/DOE] complete ; uploaded to Insignia
 7: G [JCVI/MSC] 64 contigs  ; not in AA
 8: NCTC 2916 [JCVI/MSC] 70 contigs  ; in AA
 9: str. Iwanei E [JCVI/MSC] 66 contigs ; not in AA

New (Aug 19th 2008):

 10: A2 str. Kyoto-F [LANL/JCVI/DOE] progress
 11: A3 str. Loch Maree [LANL/JCVI/DOE] complete  
 12: B str. Eklund 17B [LANL/JCVI/DOE] complete 
 13: B1 str. Okra [LANL/JCVI/DOE] complete 
 14: Ba4 str. 657 [LANL/JCVI/DOE] progress
 15: E1 str. 'BoNT E Beluga' [LANL/JCVI/DOE] progress
 16: E3 str. Alaska E43 [LANL/JCVI/DOE] complete !!! not in Insignia

File locations:

 /fs/szasmg2/Bacteria/C_botulinum/

NCBI AA assemblied:

 qc stats
 

CBCB CA3 assemblies:

                       Placed  Deg  Total
 4: Bf                     52   12     64   better than AA(fewer, avg contig len is larger)
 5: C str. Eklund          51    3     54   better than AA(fewer, avg contig len is larger)
 7: G                      47    7     54   fewer contigs than AA
 8: NCTC 2916              55   11     66   better than AA(fewer, avg contig len is larger)
 9: str. Iwanei E          44   10     55   fewer contigs than AA

 qc stats

Other links:

 * FDA
 "Clostridium botulinum is an anaerobic, Gram-positive, spore-forming rod that roduces a potent  neurotoxin. 
 The spores are heat-resistant and can survive in foods that are incorrectly or minimally processed. 
 Seven types (A, B, C, D, E, F and G) of botulism are recognized, based on the antigenic specificity of the toxin produced by each strain. 
 Types A, B, E and F cause human botulism. 
 Types C and D cause most cases of botulism in animals. 
 Animals most commonly affected are wild fowl and poultry, cattle, horses and some species of fish. 
 Although type G has been isolated from soil in Argentina, no outbreaks involving it have been recognized."

Insignia uploads

Assemblies selected:

   /fs/szasmg2/Bacteria/C_botulinum/A_ATCC_3502/best/
   /fs/szasmg2/Bacteria/C_botulinum/Bf/best/
   /fs/szasmg2/Bacteria/C_botulinum/C_str__eklund/best/
   /fs/szasmg2/Bacteria/C_botulinum/G/best/
   /fs/szasmg2/Bacteria/C_botulinum/NCTN_2916/best/
   /fs/szasmg2/Bacteria/C_botulinum/str__iwanei_e/best/