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=316273 NCBI Taxonomy] Tax ID: 316273 | |||
'''XOC : Xanthomonas oryzae pv. oryzicola BLS256; draft; NZ_AAQN00000000 ''' | '''XOC : Xanthomonas oryzae pv. oryzicola BLS256; draft; NZ_AAQN00000000 ''' | ||
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'''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 | ||
NCBI TA: 62,229 traces | NCBI TA: 62,229 traces | ||
Revision as of 17:05, 15 August 2007
XCA : Xanthomonas campestris pv. armoraciae 756C
JCVI http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=316273 NCBI Taxonomy] Tax ID: 316273
XOC : Xanthomonas oryzae pv. oryzicola BLS256; draft; NZ_AAQN00000000
JCVI
XOO : Xanthomonas oryzae pv. oryzae strain PXO99A
JCVI NCBI Taxonomy Tax ID: 360094
NCBI TA: 62,229 traces TA FTP
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
the .contig file must be updated with trace_name's