example
:
LOCUS X56730 1560 bp DNA linear PLN 30-JUN-2006
DEFINITION Yeast gene for proteasome Y13 subunit.
ACCESSION X56730
VERSION X56730.1 GI:506479
KEYWORDS proteasome.
SOURCE Saccharomyces cerevisiae (baker's yeast)
ORGANISM Saccharomyces cerevisiae
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae;
Saccharomyces.
REFERENCE 1 (bases 1 to 1560)
AUTHORS Emori,Y., Tsukahara,T., Kawasaki,H., Ishiura,S., Sugita,H. and
Suzuki,K.
TITLE Molecular cloning and functional analysis of three subunits of
yeast proteasome
JOURNAL Mol. Cell. Biol. 11 (1), 344-353 (1991)
PUBMED 1898763
REFERENCE 2
AUTHORS Emori,Y., Tsukahara,T., Kawasaki,H., Ishiura,S., Sugita,H. and
Suzuki,K.
TITLE Molecular cloning and functional analysis of three subunits of
yeast proteasome
JOURNAL Unpublished
REFERENCE 3 (bases 1 to 1560)
AUTHORS Emori,Y.
TITLE Direct Submission
JOURNAL Submitted (12-NOV-1990) Y. Emori, DEPT OF BIOPHYSICS &
BIOCHEMISTRY, FACULTY OF SCIENCE, UNIVERSITY OF TOKYO, 7-3-1 HONGO,
BUNKYO-KU, TOKYO 113, JAPAN
FEATURES Location/Qualifiers
source 1..1560
/organism="Saccharomyces cerevisiae"
/mol_type="genomic DNA"
/strain="X2180-1A"
/db_xref="taxon:4932"
TATA_signal 306..309
TATA_signal 353..356
CDS 373..1149
/codon_start=1
/product="proteasome Y13 subunit"
/protein_id="CAA40054.1"
/db_xref="GI:506480"
/db_xref="GOA:P23638"
/db_xref="InterPro:IPR000426"
/db_xref="InterPro:IPR001353"
/db_xref="InterPro:IPR016050"
/db_xref="PDB:1FNT"
/db_xref="PDB:1G0U"
/db_xref="PDB:1G65"
/db_xref="PDB:1JD2"
/db_xref="PDB:1RYP"
/db_xref="PDB:1VSY"
/db_xref="PDB:1Z7Q"
/db_xref="PDB:2F16"
/db_xref="PDB:2FAK"
/db_xref="PDB:2GPL"
/db_xref="PDB:2ZCY"
/db_xref="PDB:3BDM"
/db_xref="PDB:3D29"
/db_xref="PDB:3DY3"
/db_xref="PDB:3DY4"
/db_xref="PDB:3E47"
/db_xref="PDB:3GPJ"
/db_xref="PDB:3GPT"
/db_xref="PDB:3GPW"
/db_xref="PDB:3HYE"
/db_xref="PDB:3L5Q"
/db_xref="SGD:S000003367"
/db_xref="UniProtKB/Swiss-Prot:P23638"
/translation="MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGI
VLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTY
NEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGW
KAISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRK
GANDGEVYQKIFKPQEIKDILVKTGITKKDEDEEADEDMK"
polyA_signal 1395..1400
ORIGIN
1 ggaagaaggg tggtgttcta gcgatggtaa gattttgcca ttgcccaaag cccgataagc
61 ctatcccact tcatgaatat ataacactcg cagagctcga tgttggagac agtgagtgag
121 cagtgaattg ctcatgtttt ctctgcatcc tcatttaatg acaattagcc atgtaataac
181 atcttgaggc agttaaatat tcgttaccct gcaggtggca aaaaatttat agaataaaag
241 cataaaaaga tggatatcta tgtaataagg aaacattggc agagcgaaga gaacagactg
301 ctttctataa aaagttttcg atcagtctct attttaataa ttgattattg gatatagtta
361 gtagtgttaa acatgggttc cagaagatac gattccagga caacaatttt ctcccctgag
421 ggacgtctat atcaggttga atacgcgcta gaatccattt cacatgcagg taccgcaatt
481 gggattatgg catctgatgg gattgttctt gcagcagaac gcaaagtcac aagtacttta
541 ctagaacaag acacctctac cgaaaaactt tataagttaa acgataaaat tgcggttgcc
601 gttgctggac tgactgcaga tgcagaaatt ctaataaata cggctagaat tcacgctcaa
661 aattacctta aaacctataa tgaagatata ccagtagaaa ttttggtgag aaggctaagt
721 gatataaaac aaggttacac gcaacatggt ggtttaagac catttggtgt gtcctttatc
781 tacgccggtt atgacgatag atacggttac caattgtata catctaatcc atcgggaaac
841 tatacagggt ggaaggctat tagtgttggc gctaacacat cagcagcaca aaccctactt
901 caaatggact acaaggatga tatgaaagtc gatgatgcca ttgaactggc tttaaaaacg
961 ttatccaaaa ctaccgacag tagcgcgctg acttatgaca ggttggaatt tgctactatc
1021 agaaagggtg ctaatgacgg agaagtgtat cagaagattt tcaagcctca agagataaag
1081 gatatattgg taaagactgg tattaccaag aaggatgaag acgaagaagc tgatgaagat
1141 atgaaataag gttggaaagt attgtttgac ttcatgctta tataaatatg tacgcataga
1201 aacatatctc taaaattaaa agtgaaagaa aaaaatcgct aagattcccc tttcggggga
1261 aggctgaaga aacttttttt tgcgcaaatt tcaagatcgg aatcgctcga gaggcaaata
1321 taaaaaaggg cctgctcgtt tggcctactt gttgttggat tctaactcca atctaatttt
1381 ggcagcactt caaaaataaa caaaagcgat gtctgcgtca ctagtgaatc gatcattgaa
1441 aaatataagg aatgaattag aatttttgaa ggaatcaaac gtcatatcag gcgacatttt
1501 cgaattaatc aatagcaagt tacctgagaa atgggatgga aaccaaagat cgccccaaaa
//
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this data should store and view in hdf5 format
The example INSDC database entry is from GenBank and is shown in the GenBank format, not the EMBL format used in EMBL-Bank. Compare the representations of the entry from the INSDC member databases:
thanks for the clarification, always mix these up
what's the advantage of storing this in a HDF5 file ? and do you just want to store this as a big string or do you want to store a structured document ?
I want to store in a structured document like xml
why not using XML ? or a XML-based database like eXist ?