[Bioperl-l] load_seqdatabase.pl

Barry Moore barry.moore at genetics.utah.edu
Fri Mar 12 14:54:22 EST 2004

I'm having some trouble with load_seqdatabase.pl.  I using BioPerl 1.4 
(with some CVS updates including bioperl-db and bioperl-live Bio::DB 
yesterday), ActiveState Perl 5.8, MySQL version 12.22  distribution 
4.0.16, Windows XP.  I've successfully created a database mysql with the 
biosqldb-mysql.sql schema downloaded yesterday.  I have a file 
RefSeq_Human_mRNA_short.gb that has RefSeq mRNA in GenBank format (I 
pasted the first record from that file below).  I run 
load_seqdatabase.pl like this:

 >perl -d load_seqdatabase.pl --dbpass ******* RefSeq_Human_mRNA_short.gb

All of the script defaults should be O.K., but I've tried setting them 
all on the command line as well.

The script opens the file, and gets sequence out of it O.K., but then 
somewhere in the eval statement that begins at line 500 it heads off to 
Bio::Root::Root, and loses the plot with this error:

Undefined subroutine &Bio::Root::Root::debug called at 
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1526, 
<GEN1> line 413.

ioSQL::SeqAdaptor') called at 
tor.pm line 1507
r=HASH(0x1d22200)') called at 
tor.pm line 1386
daptor=HASH(0x1d22200)') called at load_seqdatabase.pl line 524

I'm happy to try to figure this out myself, but right now I haven't a 
clue what's going on since the subroutine &Bio::Root::Root::debug seems 
to me to be where it's supposed to be.  Is this possible a OS issue 
since I'm on Windows?  Can anyone nudge me in the right direction?

Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

LOCUS NM_000014 4577 bp mRNA linear PRI 20-DEC-2003
DEFINITION Homo sapiens alpha-2-macroglobulin (A2M), mRNA.
VERSION NM_000014.3 GI:6226959
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 4577)
AUTHORS Mathew,S., Arandjelovic,S., Beyer,W.F., Gonias,S.L. and Pizzo,S.V.
TITLE Characterization of the interaction between alpha2-macroglobulin
and fibroblast growth factor-2: the role of hydrophobic
JOURNAL Biochem. J. 374 (Pt 1), 123-129 (2003)
PUBMED 12755687
REMARK GeneRIF: FGF-2 and this protein interact at specific binding sites,
involving different FGF-2 sequences.
REFERENCE 2 (bases 1 to 4577)
AUTHORS Athauda,S.B., Nishigai,M., Arakawa,H., Ikai,A., Ukai,M. and
TITLE Inhibition of human pepsin and gastricsin by alpha2-macroglobulin
JOURNAL J Enzyme Inhib Med Chem 18 (3), 219-224 (2003)
PUBMED 14506912
REMARK GeneRIF: alpha2-macroglobulin inhibits human pepsin adn gastricsin
REFERENCE 3 (bases 1 to 4577)
AUTHORS Arandjelovic,S., Freed,T.A. and Gonias,S.L.
TITLE Growth factor-binding sequence in human alpha2-macroglobulin
targets the receptor-binding site in transforming growth
JOURNAL Biochemistry 42 (20), 6121-6127 (2003)
PUBMED 12755614
REMARK GeneRIF: alpha(2)M-derived peptides target the receptor-binding
sequence in TGF-beta
REFERENCE 4 (bases 1 to 4577)
AUTHORS Shibata,M., Sakai,H., Sakai,E., Okamoto,K., Nishishita,K.,
Yasuda,Y., Kato,Y. and Yamamoto,K.
TITLE Disruption of structural and functional integrity of alpha
2-macroglobulin by cathepsin E
JOURNAL Eur. J. Biochem. 270 (6), 1189-1198 (2003)
PUBMED 12631277
REMARK GeneRIF: These results suggest the possible involvement of
cathepsin E in disruption of the structural and functional
integrity of alpha 2-macroglobulin in the endolysosome system.
REFERENCE 5 (bases 1 to 4577)
AUTHORS Zappia,M., Cittadella,R., Manna,I., Nicoletti,G., Andreoli,V.,
Bonavita,S., Gambardella,A. and Quattrone,A.
TITLE Genetic association of alpha2-macroglobulin polymorphisms with AD
in southern Italy
JOURNAL Neurology 59 (5), 756-758 (2002)
PUBMED 12221172
REMARK GeneRIF: Genetic association of alpha2-macroglobulin polymorphisms
with Alzheimer's disease
REFERENCE 6 (bases 1 to 4577)
AUTHORS Ghebremedhin,E., Schultz,C., Thal,D.R., Del Tredici,K., Rueb,U. and
TITLE Genetic association of argyrophilic grain disease with
polymorphisms in alpha-2 macroglobulin and low-density lipoprotein
receptor-related protein genes
JOURNAL Neuropathol Appl Neurobiol 28 (4), 308-313 (2002)
PUBMED 12175343
REMARK GeneRIF: Genetic association of argyrophilic grain disease with
polymorphisms in alpha-2 macroglobulin.
REFERENCE 7 (bases 1 to 4577)
AUTHORS Kolodziej,S.J., Wagenknecht,T., Strickland,D.K. and Stoops,J.K.
TITLE The three-dimensional structure of the human alpha 2-macroglobulin
dimer reveals its structural organization in the tetrameric native
and chymotrypsin alpha 2-macroglobulin complexes
JOURNAL J. Biol. Chem. 277 (31), 28031-28037 (2002)
PUBMED 12015318
REMARK GeneRIF: The three-dimensional structure of the dimer reveals its
structural organization in the tetrameric native and chymotrypsin
alpha 2-macroglobulin complexes.
REFERENCE 8 (bases 1 to 4577)
AUTHORS McElhinney,B., Ardill,J., Caldwell,C., Lloyd,F. and McClure,N.
TITLE Ovarian hyperstimulation syndrome and assisted reproductive
technologies: why some and not others?
JOURNAL Hum. Reprod. 17 (6), 1548-1553 (2002)
PUBMED 12042276
REMARK GeneRIF: relationship between serum VEGF levels, alpha(2)M levels
and the development of OHSS in hyperstimulated subjects undergoing
REFERENCE 9 (bases 1 to 4577)
AUTHORS Mettenburg,J.M., Webb,D.J. and Gonias,S.L.
TITLE Distinct binding sites in the structure of alpha 2-macroglobulin
mediate the interaction with beta-amyloid peptide and growth
JOURNAL J. Biol. Chem. 277 (15), 13338-13345 (2002)
PUBMED 11823454
REMARK GeneRIF: distinct binding sites mediate interaction with
beta-amyloid peptide and growth factors
REFERENCE 10 (bases 1 to 4577)
AUTHORS Cvirn,G., Gallistl,S., Koestenberger,M., Kutschera,J., Leschnik,B.
and Muntean,W.
TITLE Alpha 2-macroglobulin enhances prothrombin activation and thrombin
potential by inhibiting the anticoagulant protein C/protein S
system in cord and adult plasma
JOURNAL Thromb. Res. 105 (5), 433-439 (2002)
PUBMED 12062545
REMARK GeneRIF: Alpha 2-macroglobulin enhances prothrombin activation and
thrombin potential by inhibiting the anticoagulant protein
C/protein S system in cord and adult plasma.
REFERENCE 11 (bases 1 to 4577)
AUTHORS Janka,Z., Juhasz,A., Rimanoczy,A., Boda,K., Marki-Zay,J.,
Palotas,M., Kuk,I., Zollei,M., Jakab,K. and Kalman,J.
TITLE Alpha2-macroglobulin exon 24 (Val-1000-Ile) polymorphism is not
associated with late-onset sporadic Alzheimer's dementia in the
Hungarian population
JOURNAL Psychiatr. Genet. 12 (1), 49-54 (2002)
PUBMED 11901360
REMARK GeneRIF: has an important role in the AD-specific neurodegenerative
process but its exon 24 Val-1000-Ile polymorphism is not likely to
be associated with late-onset sporadic AD in the Hungarian
REFERENCE 12 (bases 1 to 4577)
AUTHORS Chiabrando,G.A., Vides,M.A. and Sanchez,M.C.
TITLE Differential binding properties of human pregnancy zone protein-
and alpha2-macroglobulin-proteinase complexes to low-density
lipoprotein receptor-related protein
JOURNAL Arch. Biochem. Biophys. 398 (1), 73-78 (2002)
PUBMED 11811950
REMARK GeneRIF: Differential binding to ldl receptor related protein
REFERENCE 13 (bases 1 to 4577)
TITLE Alfimeprase: pharmacology of a novel fibrinolytic metalloproteinase
for thrombolysis
JOURNAL Haemostasis 31 (3-6), 141-147 (2001)
PUBMED 11910179
REMARK GeneRIF: REVIEW: binds and neutralizes alfimeprase, which has
direct proteolytic activity against the fibrinogen Aalpha chain
REFERENCE 14 (bases 1 to 4577)
TITLE Alpha 2-macroglobulin, a multifunctional binding protein with
targeting characteristics
JOURNAL FASEB J. 6 (15), 3345-3353 (1992)
PUBMED 1281457
REFERENCE 15 (bases 1 to 4577)
AUTHORS Poller,W., Faber,J.P., Klobeck,G. and Olek,K.
TITLE Cloning of the human alpha 2-macroglobulin gene and detection of
mutations in two functional domains: the bait region and the
thiolester site
JOURNAL Hum. Genet. 88 (3), 313-319 (1992)
PUBMED 1370808
REFERENCE 16 (bases 1 to 4577)
AUTHORS Poller,W., Faber,J.P. and Olek,K.
TITLE Sequence polymorphism in the human alpha-2-macroglobulin (A2M) gene
JOURNAL Nucleic Acids Res. 19 (1), 198 (1991)
PUBMED 1707161
REFERENCE 17 (bases 1 to 4577)
AUTHORS Bell,G.I., Rall,L.B., Sanchez-Pescador,R., Merryweather,J.P.,
Scott,J., Eddy,R.L. and Shows,T.B.
TITLE Human alpha 2-macroglobulin gene is located on chromosome 12
JOURNAL Somat. Cell Mol. Genet. 11 (3), 285-289 (1985)
PUBMED 2408344
REFERENCE 18 (bases 1 to 4577)
AUTHORS Kan,C.C., Solomon,E., Belt,K.T., Chain,A.C., Hiorns,L.R. and Fey,G.
TITLE Nucleotide sequence of cDNA encoding human alpha 2-macroglobulin
and assignment of the chromosomal locus
JOURNAL Proc. Natl. Acad. Sci. U.S.A. 82 (8), 2282-2286 (1985)
PUBMED 2581245
COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
reference sequence was derived from M11313.1.
On Nov 4, 1999 this sequence version replaced gi:6226762.

Summary: Alpha-2-macroglobulin is a protease inhibitor and cytokine
transporter. It inhibits many proteases, including trypsin,
thrombin and collagenase. A2M is implicated in Alzheimer disease
(AD) due to its ability to mediate the clearance and degradation of
A-beta, the major component of beta-amyloid deposits.
FEATURES Location/Qualifiers
source 1..4577
/organism="Homo sapiens"
gene 1..4577
CDS 44..4468
/note="go_function: protein carrier activity [goid
0008320] [evidence NR];
go_function: endopeptidase inhibitor activity [goid
0004866] [evidence NR];
go_function: wide-spectrum protease inhibitor activity
[goid 0017114] [evidence IEA];
go_function: serine protease inhibitor activity [goid
0004867] [evidence IEA];
go_function: alpha-2 macroglobulin [goid 0016975]
[evidence NAS];
go_process: intracellular protein transport [goid 0006886]
[evidence NR]"
/product="alpha 2 macroglobulin precursor"
sig_peptide 44..112
/note="alpha-2-macroglobulin signal peptide"
misc_feature 104..4465
/note="KOG1366; Region: Alpha-macroglobulin
[Posttranslational modification, protein turnover,
misc_feature 110..1927
/note="A2M_N; Region: Alpha-2-macroglobulin family
N-terminal region"
mat_peptide 113..4465
misc_feature 2216..4432
/note="Region: Alpha-2-macroglobulin family"
variation 1122
variation 1282
variation 1339
variation 1354
variation 1958
variation 2154
variation 2431
variation 2487
variation 2487
variation 2958
variation 3041
variation 3988
variation 4334
variation 4474
variation 4508
variation 4511
variation 4519
1 gctacaatcc atctggtctc ctccagctcc ttctttctgc aacatgggga agaacaaact
61 ccttcatcca agtctggttc ttctcctctt ggtcctcctg cccacagacg cctcagtctc
121 tggaaaaccg cagtatatgg ttctggtccc ctccctgctc cacactgaga ccactgagaa
181 gggctgtgtc cttctgagct acctgaatga gacagtgact gtaagtgctt ccttggagtc
241 tgtcagggga aacaggagcc tcttcactga cctggaggcg gagaatgacg tactccactg
301 tgtcgccttc gctgtcccaa agtcttcatc caatgaggag gtaatgttcc tcactgtcca
361 agtgaaagga ccaacccaag aatttaagaa gcggaccaca gtgatggtta agaacgagga
421 cagtctggtc tttgtccaga cagacaaatc aatctacaaa ccagggcaga cagtgaaatt
481 tcgtgttgtc tccatggatg aaaactttca ccccctgaat gagttgattc cactagtata
541 cattcaggat cccaaaggaa atcgcatcgc acaatggcag agtttccagt tagagggtgg
601 cctcaagcaa ttttcttttc ccctctcatc agagcccttc cagggctcct acaaggtggt
661 ggtacagaag aaatcaggtg gaaggacaga gcaccctttc accgtggagg aatttgttct
721 tcccaagttt gaagtacaag taacagtgcc aaagataatc accatcttgg aagaagagat
781 gaatgtatca gtgtgtggcc tatacacata tgggaagcct gtccctggac atgtgactgt
841 gagcatttgc agaaagtata gtgacgcttc cgactgccac ggtgaagatt cacaggcttt
901 ctgtgagaaa ttcagtggac agctaaacag ccatggctgc ttctatcagc aagtaaaaac
961 caaggtcttc cagctgaaga ggaaggagta tgaaatgaaa cttcacactg aggcccagat
1021 ccaagaagaa ggaacagtgg tggaattgac tggaaggcag tccagtgaaa tcacaagaac
1081 cataaccaaa ctctcatttg tgaaagtgga ctcacacttt cgacagggaa ttcccttctt
1141 tgggcaggtg cgcctagtag atgggaaagg cgtccctata ccaaataaag tcatattcat
1201 cagaggaaat gaagcaaact attactccaa tgctaccacg gatgagcatg gccttgtaca
1261 gttctctatc aacaccacca acgttatggg tacctctctt actgttaggg tcaattacaa
1321 ggatcgtagt ccctgttacg gctaccagtg ggtgtcagaa gaacacgaag aggcacatca
1381 cactgcttat cttgtgttct ccccaagcaa gagctttgtc caccttgagc ccatgtctca
1441 tgaactaccc tgtggccata ctcagacagt ccaggcacat tatattctga atggaggcac
1501 cctgctgggg ctgaagaagc tctcctttta ttatctgata atggcaaagg gaggcattgt
1561 ccgaactggg actcatggac tgcttgtgaa gcaggaagac atgaagggcc atttttccat
1621 ctcaatccct gtgaagtcag acattgctcc tgtcgctcgg ttgctcatct atgctgtttt
1681 acctaccggg gacgtgattg gggattctgc aaaatatgat gttgaaaatt gtctggccaa
1741 caaggtggat ttgagcttca gcccatcaca aagtctccca gcctcacacg cccacctgcg
1801 agtcacagcg gctcctcagt ccgtctgcgc cctccgtgct gtggaccaaa gcgtgctgct
1861 catgaagcct gatgctgagc tctcggcgtc ctcggtttac aacctgctac cagaaaagga
1921 cctcactggc ttccctgggc ctttgaatga ccaggacgat gaagactgca tcaatcgtca
1981 taatgtctat attaatggaa tcacatatac tccagtatca agtacaaatg aaaaggatat
2041 gtacagcttc ctagaggaca tgggcttaaa ggcattcacc aactcaaaga ttcgtaaacc
2101 caaaatgtgt ccacagcttc aacagtatga aatgcatgga cctgaaggtc tacgtgtagg
2161 tttttatgag tcagatgtaa tgggaagagg ccatgcacgc ctggtgcatg ttgaagagcc
2221 tcacacggag accgtacgaa agtacttccc tgagacatgg atctgggatt tggtggtggt
2281 aaactcagca ggggtggctg aggtaggagt aacagtccct gacaccatca ccgagtggaa
2341 ggcaggggcc ttctgcctgt ctgaagatgc tggacttggt atctcttcca ctgcctctct
2401 ccgagccttc cagcccttct ttgtggagct tacaatgcct tactctgtga ttcgtggaga
2461 ggccttcaca ctcaaggcca cggtcctaaa ctaccttccc aaatgcatcc gggtcagtgt
2521 gcagctggaa gcctctcccg ccttccttgc tgtcccagtg gagaaggaac aagcgcctca
2581 ctgcatctgt gcaaacgggc ggcaaactgt gtcctgggca gtaaccccaa agtcattagg
2641 aaatgtgaat ttcactgtga gcgcagaggc actagagtct caagagctgt gtgggactga
2701 ggtgccttca gttcctgaac acggaaggaa agacacagtc atcaagcctc tgttggttga
2761 acctgaagga ctagagaagg aaacaacatt caactcccta ctttgtccat caggtggtga
2821 ggtttctgaa gaattatccc tgaaactgcc accaaatgtg gtagaagaat ctgcccgagc
2881 ttctgtctca gttttgggag acatattagg ctctgccatg caaaacacac aaaatcttct
2941 ccagatgccc tatggctgtg gagagcagaa tatggtcctc tttgctccta acatctatgt
3001 actggattat ctaaatgaaa cacagcagct tactccagag gtcaagtcca aggccattgg
3061 ctatctcaac actggttacc agagacagtt gaactacaaa cactatgatg gctcctacag
3121 cacctttggg gagcgatatg gcaggaacca gggcaacacc tggctcacag cctttgttct
3181 gaagactttt gcccaagctc gagcctacat cttcatcgat gaagcacaca ttacccaagc
3241 cctcatatgg ctctcccaga ggcagaagga caatggctgt ttcaggagct ctgggtcact
3301 gctcaacaat gccataaagg gaggagtaga agatgaagtg accctctccg cctatatcac
3361 catcgccctt ctggagattc ctctcacagt cactcaccct gttgtccgca atgccctgtt
3421 ttgcctggag tcagcctgga agacagcaca agaaggggac catggcagcc atgtatatac
3481 caaagcactg ctggcctatg cttttgccct ggcaggtaac caggacaaga ggaaggaagt
3541 actcaagtca cttaatgagg aagctgtgaa gaaagacaac tctgtccatt gggagcgccc
3601 tcagaaaccc aaggcaccag tggggcattt ttacgaaccc caggctccct ctgctgaggt
3661 ggagatgaca tcctatgtgc tcctcgctta tctcacggcc cagccagccc caacctcgga
3721 ggacctgacc tctgcaacca acatcgtgaa gtggatcacg aagcagcaga atgcccaggg
3781 cggtttctcc tccacccagg acacagtggt ggctctccat gctctgtcca aatatggagc
3841 cgccacattt accaggactg ggaaggctgc acaggtgact atccagtctt cagggacatt
3901 ttccagcaaa ttccaagtgg acaacaacaa tcgcctgtta ctgcagcagg tctcattgcc
3961 agagctgcct ggggaataca gcatgaaagt gacaggagaa ggatgtgtct acctccagac
4021 ctccttgaaa tacaatattc tcccagaaaa ggaagagttc ccctttgctt taggagtgca
4081 gactctgcct caaacttgtg atgaacccaa agcccacacc agcttccaaa tctccctaag
4141 tgtcagttac acagggagcc gctctgcctc caacatggcg atcgttgatg tgaagatggt
4201 ctctggcttc attcccctga agccaacagt gaaaatgctt gaaagatcta accatgtgag
4261 ccggacagaa gtcagcagca accatgtctt gatttacctt gataaggtgt caaatcagac
4321 actgagcttg ttcttcacgg ttctgcaaga tgtcccagta agagatctca aaccagccat
4381 agtgaaagtc tatgattact acgagacgga tgagtttgca atcgctgagt acaatgctcc
4441 ttgcagcaaa gatcttggaa atgcttgaag accacaaggc tgaaaagtgc tttgctggag
4501 tcctgttctc tgagctccac agaagacacg tgtttttgta tctttaaaga cttgatgaat
4561 aaacactttt tctggtc

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