Clostridium botulinum other strains: Difference between revisions
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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] | ||
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP] | * [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP] | ||
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: | ||
[http://www.cfsan.fda.gov/~mow/chap2.html | * [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/