Xanthomonas oryzae: Difference between revisions

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XCA : Xanthomonas campestris pv. armoraciae 756C  
= XCA : Xanthomonas campestris pv. armoraciae 756C =
   [http://cpgr.tigr.org/cgi-bin/CPGR/genome_page.pl?org=Xca JCVI]
   [http://cpgr.tigr.org/cgi-bin/CPGR/genome_page.pl?org=Xca JCVI]  
  [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=329463 NCBI Taxonomy] Tax ID: 329463


XOC : Xanthomonas oryzae pv. oryzicola BLS256; draft; NZ_AAQN00000000    
= XOC : Xanthomonas oryzae pv. oryzicola BLS256; draft; NZ_AAQN00000000 =
   [http://cpgr.tigr.org/cgi-bin/CPGR/genome_page.pl?org=Xoc JCVI]
   [http://cpgr.tigr.org/cgi-bin/CPGR/genome_page.pl?org=Xoc JCVI]
  [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=129394&lvl=3&lin=f&keep=1&srchmode=1&unlock NCBI Taxonomy] Tax ID: 129394


XOO : Xanthomonas oryzae pv. oryzae strain PXO99A
= XOO : Xanthomonas oryzae pv. oryzae strain PXO99A =
   [http://cpgr.tigr.org/cgi-bin/warehouse/cpgr_warehouse.cgi JCVI]
   [http://cpgr.tigr.org/cgi-bin/warehouse/cpgr_warehouse.cgi JCVI]
   [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=360094 NCBI Taxonomy]
   [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=360094 NCBI Taxonomy] Tax ID: 360094
   62,229 TA traces
 
   AA submission dir: /fs/szasmg/Bacteria/Xanthomonas/XOO/Xoo_PXO99A/FinalAsm_June2007/AA
  NCBI TA:
   [ftp://ftp.ncbi.nih.gov/pub/TraceDB/xanthomonas_oryzae_pv__oryzae_px099a TA FTP] (not updated yet:  62,229 traces)
   65,556 traces:
    * 594    PRIMERWALK
    * 2,592  TRANSPOSONS
    * 62,370 WGS
 
  NCBI AA  
    Location: /fs/szasmg/Bacteria/Xanthomonas/XOO/Xoo_PXO99A/FinalAsm_June2007/AA
 
    $ bank2contig Xoo.bnk/ > Xoo.contig
    $ grep ^# Xoo.contig | head
    ##1106158952778_stitched 62611 5249768 bases, 00000000 checksum.
    #XOOB626TF(-939) [] 998 bases, 00000000 checksum. {11 1004} <-938 59>
    #XO1EZ18TR(-764) [] 977 bases, 00000000 checksum. {19 993} <-763 213>
    ... 
    #XO1C975TF(5248807) [RC] 875 bases, 00000000 checksum. {891 19} <5239115 5239987>
    #XO1FR06TF(5248815) [] 952 bases, 00000000 checksum. {15 964} <5239123 5240072>
 
    $ bank2fasta -b Xoo.bnk/ > Xoo.fasta (5240073 bp , 63.63 GC%)
 
    Problem : seq_name's (Ex:XOOB626TF) must be mapped to trace_name's based on the .frg file
              trace_name's must be mapped to ti's based on anc. file
              => the .contig file must contain the ti's
 
    3,327 transposon & finishing traces not present in TA : fixed 08/23/07
 
  File to submit:
    /fs/szasmg/Bacteria/Xanthomonas/XOO/Xoo_PXO99A/FinalAsm_June2007/AA/umd-20070822-120700.tar.gz
 
  [http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi?cmd=browse&ai=2956  AA]

Latest revision as of 14:04, 25 September 2008

XCA : Xanthomonas campestris pv. armoraciae 756C

 JCVI 
 NCBI Taxonomy Tax ID: 329463

XOC : Xanthomonas oryzae pv. oryzicola BLS256; draft; NZ_AAQN00000000

 JCVI
 NCBI Taxonomy Tax ID: 129394

XOO : Xanthomonas oryzae pv. oryzae strain PXO99A

 JCVI
 NCBI Taxonomy Tax ID: 360094
 NCBI TA:
 TA FTP (not updated yet:  62,229 traces)
 65,556 traces: 
   * 594    PRIMERWALK 	
   * 2,592  TRANSPOSONS
   * 62,370 WGS 
 NCBI AA 
   Location: /fs/szasmg/Bacteria/Xanthomonas/XOO/Xoo_PXO99A/FinalAsm_June2007/AA
   $ bank2contig Xoo.bnk/ > Xoo.contig
   $ grep ^# Xoo.contig | head
   ##1106158952778_stitched 62611 5249768 bases, 00000000 checksum.
   #XOOB626TF(-939) [] 998 bases, 00000000 checksum. {11 1004} <-938 59>
   #XO1EZ18TR(-764) [] 977 bases, 00000000 checksum. {19 993} <-763 213>
   ...   
   #XO1C975TF(5248807) [RC] 875 bases, 00000000 checksum. {891 19} <5239115 5239987>
   #XO1FR06TF(5248815) [] 952 bases, 00000000 checksum. {15 964} <5239123 5240072>
   $ bank2fasta -b Xoo.bnk/ > Xoo.fasta (5240073 bp , 63.63 GC%)
   Problem : seq_name's (Ex:XOOB626TF) must be mapped to trace_name's based on the .frg file
             trace_name's must be mapped to ti's based on anc. file
             => the .contig file must contain the ti's
   3,327 transposon & finishing traces not present in TA : fixed 08/23/07 
 File to submit:
   /fs/szasmg/Bacteria/Xanthomonas/XOO/Xoo_PXO99A/FinalAsm_June2007/AA/umd-20070822-120700.tar.gz
  
 AA