Yersinia pestis: Difference between revisions

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NCBI
== Data ==
 
=== NCBI ===
 
  [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Yersinia%20pestis 16(7)  Genome projects]


Genome projects:
Genome projects:
     1  Yersinia pestis Angola [TIGR]
     1  Yersinia pestis Angola [TIGR] complete, in AA (Aug 19th 2008)
     2C Yersinia pestis Antiqua [DOE Joint Genome Institute] complete
     2C Yersinia pestis Antiqua [DOE Joint Genome Institute] complete
     3  Yersinia pestis CA88-4125 [ERIC/Joint Genome Institute, Production
     3  Yersinia pestis CA88-4125 [ERIC/Joint Genome Institute, Production
Line 28: Line 32:
   15 yersinia_pestis_biovar_orientalis_str__ip275
   15 yersinia_pestis_biovar_orientalis_str__ip275
   16 yersinia_pestis_biovar_orientalis_str__mg05-1020
   16 yersinia_pestis_biovar_orientalis_str__mg05-1020
AA:
        Assembly Name                                          Subm.  AI      TaxID  Length(bp)      #Ctgs  #Traces  Coverage  Comment
    9  Yersinia pestis biovar Antiqua str. B42003004          TIGR    2707    404215  4,841,690      69      72,466  13.0X    contigs have many linking mates
    10  Yersinia pestis biovar Antiqua str. E1979001            TIGR    2607    360099  4,847,813      75      66,096  11.9X
    11  Yersinia pestis biovar Antiqua str. UG05-0454          TIGR    2605    404218  4,838,246      98      72,523  12.3X
    12  Yersinia pestis biovar Mediaevalis str. K1973002        TIGR    2618    404216  4,720,694      73      64,204  11.3X
    14  Yersinia pestis biovar Orientalis str. F1991016        TIGR    2774    404214  4,892,085      107    65,394  11.6X
    15  Yersinia pestis biovar Orientalis str. IP275            TIGR    1019    373665  5,081,206      274    45,934  7.6X
    16  Yersinia pestis biovar Orientalis str. MG05-1020        TIGR    2608    404217  4,977,609      80      71,897  12.1X
=== DOE ===
  [http://genome.jgi-psf.org/mic_home.html Microbial Genomes] (assembly seq, no traces)
=== Sanger ===
  [http://www.sanger.ac.uk/Projects/Y_pestis/ Genome project] (assembly seq, no traces)
== Assemblies ==
=== Yersinia pestis angola ===
  TIGR
  Not in AA !!
  Assembled with CA4, default params
  /fs/szasmg2/Bacteria/Yersinia_pestis/yersinia_pestis_angola/2007_1128_CA
  1 large scaff; many small(<5KB) contigs; some large/deep cvg degen that aligned to related finished plasmids
  lots of missoriented mates (from all libs); one pile of linking mates; decreasing erate to 0.5% did not generate a better assembly
=== Yersinia pestis biovar Antiqua str. B42003004 ===
AA:
  /fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2707 : 69 contigs that have lots of linking mates at the ends
CBCB assembly:
  /fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2707/2007_1124_CA : sacffolds have lots of missoriented mates
  8 scaff, 34 contigs, 1 degen
  Tried erate=0.5% => no improvement
  alignment to '''Yersinia pestis biovar Microtus str. 91001(complete)''' has many breaks
=== Yersinia pestis biovar Antiqua str. E1979001 ===
AA:
  /fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2607 : 75 contigs that have lots of linking mates at the ends
CBCB assembly:
  /fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2607/2007_1128_CA : sacffolds have lots of missoriented mates
  8 scaff, 29 contigs, 6 degens
  Tried erate=0.5% => no improvement
=== Yersinia pestis biovar Microtus str. 91001 ===
China, Not in AA
  Name          Length %GC    Description
  NC_005810.1    4595065 47.65  Yersinia pestis biovar Microtus str. 91001, complete genome
  NC_005813.1    70159  44.85  Yersinia pestis biovar Microtus str. 91001 plasmid pCD1, complete sequence
  NC_005814.1    21742  49.07  Yersinia pestis biovar Microtus str. 91001 plasmid pCRY, complete sequence
  NC_005815.1    106642 50.31  Yersinia pestis biovar Microtus str. 91001 plasmid pMT1, complete sequence
  NC_005816.1    9609  45.26  Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1,complete sequence
  total          4803217

Latest revision as of 17:46, 19 August 2008

Data

NCBI

 16(7)  Genome projects

Genome projects: 

    1  Yersinia pestis Angola [TIGR] complete, in AA (Aug 19th 2008)
    2C Yersinia pestis Antiqua [DOE Joint Genome Institute] complete
    3  Yersinia pestis CA88-4125 [ERIC/Joint Genome Institute, Production
    4C Yersinia pestis CO92 [Sanger Institute] complete
    5  Yersinia pestis FV-1 [TGen]
    6C Yersinia pestis KIM [University of Wisconsin-Madison ...] complete
    7C  Yersinia pestis Nepal516 [DOE Joint Genome Institute] complete
    8C Yersinia pestis Pestoides F [DOE Joint Genome Institute] complete
    9  Yersinia pestis biovar Antiqua str. B42003004 [TIGR]
   10  Yersinia pestis biovar Antiqua str. E1979001 [TIGR]
   11  Yersinia pestis biovar Antiqua str. UG05-0454 [TIGR]
   12  Yersinia pestis biovar Mediaevalis str. K1973002 [TIGR]
   13C Yersinia pestis biovar Microtus str. 91001 [Academy of Military Medical Sciences China] complete
   14  Yersinia pestis biovar Orientalis str. F1991016 [TIGR]
   15  Yersinia pestis biovar Orientalis str. IP275 [TIGR]
   16  Yersinia pestis biovar Orientalis str. MG05-1020 [TIGR]

TA: 

   1 yersinia_pestis_angola
   9 yersinia_pestis_biovar_antiqua_str__b42003004
  10 yersinia_pestis_biovar_antiqua_str__e1979001
  11 yersinia_pestis_biovar_antiqua_str__ug05-0454
  12 yersinia_pestis_biovar_mediaevalis_str__k1973002
  14 yersinia_pestis_biovar_orientalis_str__f1991016
  15 yersinia_pestis_biovar_orientalis_str__ip275
  16 yersinia_pestis_biovar_orientalis_str__mg05-1020

AA: 

       Assembly Name                                           Subm.   AI      TaxID   Length(bp)      #Ctgs  #Traces  Coverage  Comment
    9  Yersinia pestis biovar Antiqua str. B42003004           TIGR    2707    404215  4,841,690       69      72,466  13.0X     contigs have many linking mates
   10  Yersinia pestis biovar Antiqua str. E1979001            TIGR    2607    360099  4,847,813       75      66,096  11.9X
   11  Yersinia pestis biovar Antiqua str. UG05-0454           TIGR    2605    404218  4,838,246       98      72,523  12.3X
   12  Yersinia pestis biovar Mediaevalis str. K1973002        TIGR    2618    404216  4,720,694       73      64,204  11.3X
   14  Yersinia pestis biovar Orientalis str. F1991016         TIGR    2774    404214  4,892,085       107     65,394  11.6X
   15  Yersinia pestis biovar Orientalis str. IP275            TIGR    1019    373665  5,081,206       274     45,934  7.6X
   16  Yersinia pestis biovar Orientalis str. MG05-1020        TIGR    2608    404217  4,977,609       80      71,897  12.1X

DOE

 Microbial Genomes (assembly seq, no traces)

Sanger

 Genome project (assembly seq, no traces)

Assemblies

Yersinia pestis angola

 TIGR
 Not in AA !!
 Assembled with CA4, default params
 /fs/szasmg2/Bacteria/Yersinia_pestis/yersinia_pestis_angola/2007_1128_CA
 1 large scaff; many small(<5KB) contigs; some large/deep cvg degen that aligned to related finished plasmids
 lots of missoriented mates (from all libs); one pile of linking mates; decreasing erate to 0.5% did not generate a better assembly

Yersinia pestis biovar Antiqua str. B42003004

AA: 

 /fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2707 : 69 contigs that have lots of linking mates at the ends

CBCB assembly: 

 /fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2707/2007_1124_CA : sacffolds have lots of missoriented mates
 8 scaff, 34 contigs, 1 degen
 Tried erate=0.5% => no improvement
 alignment to Yersinia pestis biovar Microtus str. 91001(complete) has many breaks

Yersinia pestis biovar Antiqua str. E1979001

AA: 

 /fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2607 : 75 contigs that have lots of linking mates at the ends

CBCB assembly: 

 /fs/szasmg2/Bacteria/Yersinia_pestis/AA/CS--AI-2607/2007_1128_CA : sacffolds have lots of missoriented mates
 8 scaff, 29 contigs, 6 degens
 Tried erate=0.5% => no improvement

Yersinia pestis biovar Microtus str. 91001

China, Not in AA 

 Name           Length %GC    Description 
 NC_005810.1    4595065 47.65  Yersinia pestis biovar Microtus str. 91001, complete genome
 NC_005813.1    70159  44.85  Yersinia pestis biovar Microtus str. 91001 plasmid pCD1, complete sequence
 NC_005814.1    21742  49.07  Yersinia pestis biovar Microtus str. 91001 plasmid pCRY, complete sequence
 NC_005815.1    106642 50.31  Yersinia pestis biovar Microtus str. 91001 plasmid pMT1, complete sequence
 NC_005816.1    9609   45.26  Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1,complete sequence
 total          4803217
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