Clostridium perfringens: Difference between revisions
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Summary: | |||
~ 10 strains in NCBI Taxonomy | |||
8 genome projects | |||
2 complete genomes | |||
7 assemblies in NCBI AA (all TIGR/JCVI) | |||
7 trace sets (all TIGR/JCVI) | |||
== Data sources == | == Data sources == | ||
'''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= | * [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] | ||
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 | ||
| Line 18: | Line 22: | ||
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/ | ||
File locations: | File locations: | ||
/fs/szasmg2/Bacteria/C_perfringens | /fs/szasmg2/Bacteria/C_perfringens | ||
NCBI AA assemblied: | |||
* [[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 | ||
| Line 37: | Line 47: | ||
9. SM101 29 120 140 | 9. SM101 29 120 140 | ||
10. 13 | 10. 13 | ||
* [[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 == | ||
/fs/szasmg2/Bacteria/C_perfringens/ATCC_13124/AA/ | Location: /fs/szasmg2/Bacteria/C_perfringens/ATCC_13124/ | ||
AA contigs: | |||
Name Length %GC | |||
1 3256683 28.38 | |||
Reads: | |||
WGA 51622 | |||
FINISHING 2521 | |||
Total 54143 | |||
* No reads align to SM101 plasmids | |||
== 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: | |||
WGA 40816 | |||
FINISHING 2994 | |||
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/ | |||
Latest revision as of 17:56, 19 August 2008
Summary:
~ 10 strains in NCBI Taxonomy 8 genome projects 2 complete genomes 7 assemblies in NCBI AA (all TIGR/JCVI) 7 trace sets (all TIGR/JCVI)
Data sources
NCBI:
Strains:
1. A: not sequenced
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
4. C str. JGS1495: JCVI, 40K reads, 84 contigs
5. CPE str. F4969: JCVI, 37K reads, 74 contig
6. D: not sequenced
7. E str. JGS1987: JCVI, 38K reads, 101 contigs
8. NCTC 8239: JCVI, 38K reads, 55 contigs
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); uploaded to Insignia
password protected web site : http://kantaro2.grt.kyushu-u.ac.jp/microb/welch/
File locations:
/fs/szasmg2/Bacteria/C_perfringens
NCBI AA assemblied:
ATCC_13124 : many missoriented reads
CBCB CA3 assemblies:
Placed Deg Total 1. A 2. ATCC_13124 37 69 106 3. B_str__ATCC_362 64 65 129 4. C_str__JGS1495 53 39 92 5. CPE_str__F4969 60 4 64 better 6. D 7. E_str__JGS1987 78 15 83 better 8. str__nctc8239 48 2 50 better 9. SM101 29 120 140 10. 13
Other links:
* FDA
ATCC_13124
Location: /fs/szasmg2/Bacteria/C_perfringens/ATCC_13124/
AA contigs:
Name Length %GC 1 3256683 28.38
Reads:
WGA 51622 FINISHING 2521 Total 54143 * No reads align to SM101 plasmids
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:
WGA 40816 FINISHING 2994 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/