Clostridium botulinum other strains: Difference between revisions

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!!! OLD; should be deleted
Other than the Sanger sequenced Hall strain A (ATCC 3502)
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 ==
== Data sources ==
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* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1491 Tax Browser]
* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1491 Tax Browser]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=search&term=Clostridium%20botulinum Genome Projects]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=search&term=Clostridium%20botulinum Genome Projects]
Strains:
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP]
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP]


Strains:
Genome projects:
   1. A str. ATCC 19397 [LANL/JCVI/DOE] complete  
   1. A str. ATCC 19397 [LANL/JCVI/DOE] complete ; uploaded to Insignia
   2*: A str. ATCC 3502 [Sanger] complete  
   2*: A str. ATCC 3502 [Sanger] complete ; uploaded to Insignia
   3: A str. Hall [LANL/JCVI/DOE] complete  
   3: A str. Hall [LANL/JCVI/DOE] complete ; uploaded to Insignia
   4: Bf [JCVI/MSC] 70 contigs ; in AA
   4: Bf [JCVI/MSC] 70 contigs ; in AA
   5: C str. Eklund [JCVI/MSC] 76 contigs  ; in AA
   5: C str. Eklund [JCVI/MSC] 76 contigs  ; in AA
   6: F str. Langeland plasmid pCLI [LANL/JCVI/DOE] complete
   6: F str. Langeland plasmid pCLI [LANL/JCVI/DOE] complete ; uploaded to Insignia
   7: G [JCVI/MSC] 64 contigs  ; not in AA
   7: G [JCVI/MSC] 64 contigs  ; not in AA
   8: NCTC 2916 [JCVI/MSC] 70 contigs  ; in AA
   8: NCTC 2916 [JCVI/MSC] 70 contigs  ; in AA
   9: str. Iwanei E [JCVI/MSC] 66 contigs
   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:
File locations:
   /fs/szasmg2/Bacteria/C_botulinum/
   /fs/szasmg2/Bacteria/C_botulinum/
NCBI AA assemblied:
  [[Media:C_botulinum.AA.qc.combine|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
  [[Media:C_botulinum.2007_1005_WGA.qc.combine|qc stats]]


Other links:
Other links:
Line 34: Line 62:
   Animals most commonly affected are wild fowl and poultry, cattle, horses and some species of fish.  
   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."
   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/

Latest revision as of 17:04, 8 December 2008

!!! 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:

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/