Clostridium perfringens - Revision history

Dpuiu at 17:56, 19 August 2008

2008-08-19T17:56:34Z

← Older revision		Revision as of 17:56, 19 August 2008
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	~ 10 strains in NCBI Taxonomy		~ 10 strains in NCBI Taxonomy
	8 genome projects		8 genome projects
	3 complete genomes		2 complete genomes
	7 assemblies in NCBI AA (all TIGR/JCVI)		7 assemblies in NCBI AA (all TIGR/JCVI)
	7 trace sets (all TIGR/JCVI)		7 trace sets (all TIGR/JCVI)

2008-01-15T21:13:00Z

Data sources

← Older revision		Revision as of 21:13, 15 January 2008
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	Strains:		Strains:
	1. A: not sequenced		1. A: not sequenced
	2. ATCC 13124: JCVI; 54K reads, 1 contig ; finished; 3,256,683 bp ;28.38% GC ; ??? what about plasmids		2. ATCC 13124: JCVI; 54K reads, 1 contig ; finished; 3,256,683 bp ;28.38% GC ; ??? what about plasmids ; uploaded to Insignia
	3. B str. ATCC 3626: JCVI, 38K reads, 98 contigs		3. B str. ATCC 3626: JCVI, 38K reads, 98 contigs
	4. C str. JGS1495: JCVI, 40K reads, 84 contigs		4. C str. JGS1495: JCVI, 40K reads, 84 contigs
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	7. E str. JGS1987: JCVI, 38K reads, 101 contigs		7. E str. JGS1987: JCVI, 38K reads, 101 contigs
	8. NCTC 8239: JCVI, 38K reads, 55 contigs		8. NCTC 8239: JCVI, 38K reads, 55 contigs
	9. SM101: JCVI+TIGR, 43K reads, 3 contigs (chromosome+2 plasmids) (finished)		9. SM101: JCVI+TIGR, 43K reads, 3 contigs (chromosome+2 plasmids) (finished) ; uploaded to Insignia
	10. 13: University of Tsukuba Japan, 52K reads (not available in NCBI TA), 2 contigs(chomosome+plasmid), phrap assembly (finished);		10. 13: University of Tsukuba Japan, 52K reads (not available in NCBI TA), 2 contigs(chomosome+plasmid), phrap assembly (finished); uploaded to Insignia
	password protected web site : http://kantaro2.grt.kyushu-u.ac.jp/microb/welch/		password protected web site : http://kantaro2.grt.kyushu-u.ac.jp/microb/welch/

2007-12-05T16:42:28Z

← Older revision		Revision as of 16:42, 5 December 2007
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	FINISHING 2994		FINISHING 2994
	Total 543810		Total 543810

			== Insignia uploads ==

			Assemblies selected:
			/fs/szasmg2/Bacteria/C_perfringens/ATCC_13124/best -> AA/CS--AI-1565/
			/fs/szasmg2/Bacteria/C_perfringens/B_str__ATCC_3626/best -> AA/CS--AI-2899/
			/fs/szasmg2/Bacteria/C_perfringens/CPE_str__F4969/best -> 2007_1005_WGA/
			/fs/szasmg2/Bacteria/C_perfringens/C_str__JGS1495/best -> AA/CS--AI-2889/
			/fs/szasmg2/Bacteria/C_perfringens/E_str__JGS1987/best -> 2007_1005_WGA
			/fs/szasmg2/Bacteria/C_perfringens/SM101/best -> AA/CS--AI-1688/
			/fs/szasmg2/Bacteria/C_perfringens/str__nctc8239/best -> 2007_1005_WGA/

2007-11-26T21:00:35Z

Data sources

← Older revision		Revision as of 21:00, 26 November 2007
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	* [[Media:C_perfringens.AA.qc.combine\|qc stats]]		* [[Media:C_perfringens.AA.qc.combine\|qc stats]]

			ATCC_13124 : many missoriented reads

	CBCB CA3 assemblies:		CBCB CA3 assemblies:
	Placed Deg Total		Placed Deg Total
	1. A		1. A
	2. ATCC_13124 37 69 106		2. ATCC_13124 37 69 106

2007-10-18T16:07:44Z

← Older revision		Revision as of 16:07, 18 October 2007
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			Summary:
			~ 10 strains in NCBI Taxonomy
			8 genome projects
			3 complete genomes
			7 assemblies in NCBI AA (all TIGR/JCVI)
			7 trace sets (all TIGR/JCVI)

	== Data sources ==		== Data sources ==

2007-10-18T16:04:02Z

← Older revision		Revision as of 16:04, 18 October 2007
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	'''NCBI:'''		'''NCBI:'''
	* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1502 Tax Browser]		* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1502 Tax Browser]
	* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12308 Genome Projects]
	* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Clostridium%perfringens Genome Projects]		* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Clostridium%perfringens Genome Projects]
	* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP]		* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP]

2007-10-18T16:03:35Z

← Older revision		Revision as of 16:03, 18 October 2007
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	* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1502 Tax Browser]		* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1502 Tax Browser]
	* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12308 Genome Projects]		* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12308 Genome Projects]
			* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Clostridium%perfringens Genome Projects]
	* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP]		* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP]

2007-10-17T17:46:16Z

Data sources

← Older revision		Revision as of 17:46, 17 October 2007
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	* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1502 Tax Browser]		* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1502 Tax Browser]
	* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12308 Genome Projects]		* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12308 Genome Projects]

	~~Strains:~~

	* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP]		* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ NCBI_TA_FTP]

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	* [[Media:C_perfringens.2007_1005_WGA.qc.combine\|qc stats]]		* [[Media:C_perfringens.2007_1005_WGA.qc.combine\|qc stats]]

			Other links:
			* [http://www.cfsan.fda.gov/~mow/chap11.html FDA]

	== ATCC_13124 ==		== ATCC_13124 ==

2007-10-16T19:21:16Z

ATCC_13124

← Older revision		Revision as of 19:21, 16 October 2007
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	Location: /fs/szasmg2/Bacteria/C_perfringens/ATCC_13124/		Location: /fs/szasmg2/Bacteria/C_perfringens/ATCC_13124/

			AA contigs:
			Name Length %GC
			1 3256683 28.38

	Reads:		Reads:
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	FINISHING 2521		FINISHING 2521
	Total 54143		Total 54143
			* No reads align to SM101 plasmids

	== SM101 ==		== SM101 ==

2007-10-16T19:19:49Z

SM101

← Older revision		Revision as of 19:19, 16 October 2007
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	Location: /fs/szasmg2/Bacteria/C_perfringens/SM101		Location: /fs/szasmg2/Bacteria/C_perfringens/SM101

			AA contigs:
			Name Length %GC
			1 12397 26.68
			2 12206 25.82
			3 2897393 28.25

	Reads:		Reads: