[Biojava-l] RefSeq bioJava parser problem
wanner.de@pg.com
wanner.de@pg.com
Thu, 9 May 2002 08:38:51 -0400
bioJava members,
Our Genbank parser using bioJava has been working great. We've now been asked
to parse RefSeq accession numbers..... which seem to have only minor differences
in the Genbank format, however, bioJava cannot read the sequence. I get the
" org.biojava.bio.BioException: Could not read sequence" exception. Below is
the sequence I am trying to parse (downloaded from NCBI): Do you have any
ideas ? Sould we be
using something other than a Genbank reader to be parsing this?
Thanks Much,
LOCUS NP_000221 167 aa linear PRI 29-JAN-2002
DEFINITION leptin precursor; leptin (murine obesity homolog); obesity; obesity
(murine homolog, leptin) [Homo sapiens].
ACCESSION NP_000221
PID g4557715
VERSION NP_000221.1 GI:4557715
DBSOURCE REFSEQ: accession NM_000230.1
KEYWORDS .
SOURCE human.
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE 1 (residues 1 to 167)
AUTHORS Friedman JM, Leibel RL, Siegel DS, Walsh J and Bahary N.
TITLE Molecular mapping of the mouse ob mutation
JOURNAL Genomics 11 (4), 1054-1062 (1991)
MEDLINE 92147101
PUBMED 1686014
REFERENCE 2 (residues 1 to 167)
AUTHORS Zhang Y, Proenca R, Maffei M, Barone M, Leopold L and Friedman JM.
TITLE Positional cloning of the mouse obese gene and its human homologue
JOURNAL Nature 372 (6505), 425-432 (1994)
MEDLINE 95075453
PUBMED 7984236
REMARK Erratum:[[published erratum appears in Nature 1995 Mar
30;374(6521):479]]
REFERENCE 3 (residues 1 to 167)
AUTHORS Masuzaki H, Ogawa Y, Isse N, Satoh N, Okazaki T, Shigemoto M, Mori
K, Tamura N, Hosoda K, Yoshimasa Y et al.
TITLE Human obese gene expression. Adipocyte-specific expression and
regional differences in the adipose tissue
JOURNAL Diabetes 44 (7), 855-858 (1995)
MEDLINE 95309556
PUBMED 7789654
REFERENCE 4 (residues 1 to 167)
AUTHORS Green ED, Maffei M, Braden VV, Proenca R, DeSilva U, Zhang Y, Chua
SC Jr, Leibel RL, Weissenbach J and Friedman JM.
TITLE The human obese (OB) gene: RNA expression pattern and mapping on
the physical, cytogenetic, and genetic maps of chromosome 7
JOURNAL Genome Res. 5 (1), 5-12 (1995)
MEDLINE 96352898
PUBMED 8717050
REFERENCE 5 (residues 1 to 167)
AUTHORS Isse N, Ogawa Y, Tamura N, Masuzaki H, Mori K, Okazaki T, Satoh N,
Shigemoto M, Yoshimasa Y, Nishi S et al.
TITLE Structural organization and chromosomal assignment of the human
obese gene
JOURNAL J. Biol. Chem. 270 (46), 27728-27733 (1995)
MEDLINE 96070903
PUBMED 7499240
REFERENCE 6 (residues 1 to 167)
AUTHORS Gong,D.W., Bi,S., Pratley,R.E. and Weintraub,B.D.
TITLE Genomic structure and promoter analysis of the human obese gene
JOURNAL J. Biol. Chem. 271 (8), 3971-3974 (1996)
MEDLINE 96223958
REFERENCE 7 (residues 1 to 167)
AUTHORS Niki T, Mori H, Tamori Y, Kishimoto-Hashirmoto M, Ueno H, Araki S,
Masugi J, Sawant N, Majithia HR, Rais N et al.
TITLE Human obese gene: molecular screening in Japanese and Asian Indian
NIDDM patients associated with obesity
JOURNAL Diabetes 45 (5), 675-678 (1996)
MEDLINE 96198511
PUBMED 8621021
REFERENCE 8 (residues 1 to 167)
AUTHORS Comuzzie,A.G., Hixson,J.E., Almasy,L., Mitchell,B.D., Mahaney,M.C.,
Dyer,T.D., Stern,M.P., MacCluer,J.W. and Blangero,J.
TITLE A major quantitative trait locus determining serum leptin levels
and fat mass is located on human chromosome 2
JOURNAL Nat. Genet. 15 (3), 273-276 (1997)
MEDLINE 97207647
PUBMED 9054940
REFERENCE 9 (residues 1 to 167)
AUTHORS Clement,K., Vaisse,C., Lahlou,N., Cabrol,S., Pelloux,V.,
Cassuto,D., Gourmelen,M., Dina,C., Chambaz,J., Lacorte,J.M.,
Basdevant,A., Bougneres,P., Lebouc,Y., Froguel,P. and Guy-Grand,B.
TITLE A mutation in the human leptin receptor gene causes obesity and
pituitary dysfunction
JOURNAL Nature 392 (6674), 398-401 (1998)
MEDLINE 98196670
PUBMED 9537324
REFERENCE 10 (residues 1 to 167)
AUTHORS Friedman,J.M. and Halaas,J.L.
TITLE Leptin and the regulation of body weight in mammals
JOURNAL Nature 395 (6704), 763-770 (1998)
MEDLINE 99010835
COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
reference sequence was derived from U43653.1.
Summary: This gene is similar to the mouse obesity gene (ob). The
protein encoded by this gene is secreted by white adipocytes. In
the mouse study, mutations in this gene are linked to severe and
morbid obesity.
FEATURES Location/Qualifiers
source 1..167
/organism="Homo sapiens"
/db_xref="taxon:9606"
/chromosome="7"
/map="7q31.3"
Protein 1..167
/product="leptin precursor"
/note="leptin (murine obesity homolog); obesity (murine
homolog, leptin)"
sig_peptide 1..21
Region 22..167
/region_name="Leptin"
/note="Leptin"
/db_xref="CDD:pfam02024"
mat_peptide 22..167
/product="leptin"
CDS 1..167
/gene="LEP"
/coded_by="NM_000230.1:57..560"
/db_xref="LocusID:3952"
/db_xref="MIM:164160"
ORIGIN
1 mhwgtlcgfl wlwpylfyvq avpiqkvqdd tktliktivt rindishtqs vsskqkvtgl
61 dfipglhpil tlskmdqtla vyqqiltsmp srnviqisnd lenlrdllhv lafskschlp
121 wasgletlds lggvleasgy stevvalsrl qgslqdmlwq ldlspgc
//