Difference between revisions of "Clostridium perfringens"

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(Data sources)
 
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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=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]
 
 
Strains:
 
 
 
 
* [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
+
   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:
 +
                    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
 +
 +
* [[Media:C_perfringens.2007_1005_WGA.qc.combine|qc stats]]
 +
 +
Other links:
 +
  * [http://www.cfsan.fda.gov/~mow/chap11.html 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/

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/