[Bioperl-l] How can i get lines without tag, next to organism
Fabiola Sánchez
fsanchez at cifn.unam.mx
Mon Oct 6 14:30:17 EDT 2003
Hello!
I'm reading files in genbank format
i want to parser the lines below or next to organism, but these don't
have tag
how can i get this
i can get organism but i can't get the lines next to organism
for example:
ORGANISM Pseudospirillum japonicum
Bacteria; Proteobacteria; Gammaproteobacteria;
Oceanospirillales;
Pseudospirillum.
I need to get:
Bacteria; Proteobacteria; Gammaproteobacteria;
Oceanospirillales;
Pseudospirillum.
Thank you.
Fabi
LOCUS AB006766 1459 bp DNA linear BCT
13-FEB-1999
DEFINITION Oceanospirillum japonicum gene for 16S rRNA, partial sequence,
strain:IFO19191.
ACCESSION AB006766
VERSION AB006766.1 GI:4049363
KEYWORDS 16S ribosomal RNA.
SOURCE Pseudospirillum japonicum
ORGANISM Pseudospirillum japonicum
Bacteria; Proteobacteria; Gammaproteobacteria;
Oceanospirillales;
Pseudospirillum.
REFERENCE 1 (sites)
AUTHORS Satomi,M., Kimura,B., Hayashi,M., Shouzen,Y., Okuzumi,M. and
Fujii,T.
TITLE Marinospirillum gen. nov., with descriptions of Marinospirillum
megaterium sp. nov., isolated from kusaya gravy, and transfer of
Oceanospirillum minutulum to Marinospirillum minutulum comb. nov
JOURNAL Int. J. Syst. Bacteriol. 48 Pt 4, 1341-1348 (1998)
MEDLINE 99045875
PUBMED 9828435
REFERENCE 2 (bases 1 to 1459)
AUTHORS Satomi,M.
TITLE Direct Submission
JOURNAL Submitted (20-AUG-1997) Masataka Satomi, National Reserch
Institute
of Fisheries Science, Food Processing and Preservation Division;
Fukuura 2-12-4, Kanazawa-ku,, Yokohama, Kanagawa 236, Japan
(E-mail:msatomi at nrifs.affrc.go.jp, Tel:81-45-788-7670,
Fax:81-45-788-7670)
FEATURES Location/Qualifiers
source 1..1459
/organism="Pseudospirillum japonicum"
/mol_type="genomic DNA"
/strain="ATCC19191"
/db_xref="taxon:64971"
rRNA <1..>1459
/product="16S ribosomal RNA"
BASE COUNT 368 a 326 c 462 g 302 t 1 others
ORIGIN
1 attgaacgct ggcggcaggc ctaacacatg caagtcgagc ggcagcgggg agtagcttgc
61 tactttgccg gcgagcggcg gacgggtgag taacgcatag gaatctgccc agtagagggg
121 gatagccagg ggaaactctg attaataccg catacgccct acgggggaaa aggggctttt
181 agctcctgct attggatgag cctatgtcgg attagctagt tggtagggta aaggcctacc
241 aaggcgacga tccgtagctg ttctgagagg atgatcagcc acactgggac tgagacacgg
301 cccagactcc tacgggaggc agcagtgggg aatattgcac aatgggggga accctgatgc
361 acccatcccg cgtgtgtgaa gaaggccttc gggttgtaaa gcactttcag caaggaggaa
421 ggccgtatgc ttaataggca tgcggattga cgttacttgc agaagaagca ccggctaact
481 ccgtgccagc agccgcggta atacggaggg tgcgagcgtt aatcggaatt actgggcgta
541 aagcgcgcgt aggcggatag gtcagtcaga tgtgaaagcc ctgggctcaa cctaggacgt
601 gcacctgata ctgcttatct agagtaaggt agagggtagt agaatttcct gtgtagcggt
661 gaaatgcgta gatataggaa ggaataccgg tggcgaaggc ggctacctgg actattactg
721 acgctgaggt gcgaaagcgt ggggatcaaa caggattaga taccctggta gtccacgctg
781 taaacgatgt cgactagccg ttgccgacct tgagttggga gtggcgcagc taacgcgata
841 agtcgaccgc ctggggagta cggccgcaag gttaaaactc aaatgaattg acgggggccc
901 gcacaagcgg tggagcatgt ggtttaattc gatgcaacgc gaagaacctt acctactctt
961 gacatccaga gaactttcca gagatggata ggtgccttcg ggaactctga gacaggtgct
1021 gcatggctgt cgtcagctcg tgttgtgaaa tgttgggtta agtcccgtaa cgagcgcaac
1081 ccttatcctt atttgccagc gggttatgcc gggaacttta aggaaactgc cggtgacaaa
1141 ccggaggaag gtggggacga cgtcaagtca tcatggccct tacgagtagg gctacacacg
1201 tgctacaatg gtaagtacag agggttgcaa gaccgcgagg tggagctaat ctcagaaaac
1261 ttatcgtagt ccggattgga gtctgcaact cgactccatg aagtcggaat cgctagtaat
1321 cgcgaatcag aatgtcgcgg tgaatacgtt cccgggcctt gtacacaccg cccgtcacac
1381 catgggagtg gacttcacca gaagtagtta gtctaaccgn aagggggacg attaccacgg
1441 tggggttcat gactggggt
//
More information about the Bioperl-l
mailing list