Xanthomonas oryzae: Difference between revisions
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= XCA : Xanthomonas campestris pv. armoraciae 756C = | |||
[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 | |||
[http://cpgr.tigr.org/cgi-bin/warehouse/cpgr_warehouse.cgi JCVI | = XOC : Xanthomonas oryzae pv. oryzicola BLS256; draft; NZ_AAQN00000000 = | ||
[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 = | |||
[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] Tax ID: 360094 | |||
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