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:
  * [http://www.cfsan.fda.gov/~mow/chap2.html 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/

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/