I fetched(gcg9) the following accession from the genbank database: =
AA390074. The sequence in the record fetch returns is incorrect, =
however the rest of the record IS correct. Below are two copies =
of the genbank record, one from retrieve at ncbi and one fetched from =
the gb_est11 GCG formatted database. I looked at the flat file =
(gb_est11.seq - created when formatting the GCG database) and the =
sequence there is identical to the one sent back by retrieve. I =
grep'd flat file (gb_est11.seq) with the first 30 nt of the =
sequence returned by fetch and did not get a string match. I also =
grep'd the other est flat files for the 1st 20 nt and did not get =
a match. Also, when I search the dbest with the sequence =
returned by fetch there is no exact match, but there is an exact =
match to the sequence returned by retrieve. Has anyone heard of =
this happening before? I do not think that I have made any errors =
converting the GenBank db to GCG. Any ideas??
Thanks,
Chris
>Subject: Results-RETRIEVE Server:
>Reply-To: Retrieve Server <retrieve at ncbi.nlm.nih.gov>
>From: RETRIEVE E-Mail Server <retrieve at ncbi.nlm.nih.gov>
>Status: RO
>=
>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D
>To Obtain Help Documentation: send e-mail to =
'retrieve at ncbi.nlm.nih.gov'
> with the word 'help' in the body of the mail message.
>>Note: GenBank retrieval and submission tools are available =
through
> the World Wide Web at the URL: <http://www.ncbi.nlm.nih.gov/ =
For more
> information contact User Services at: info at ncbi.nlm.nih.gov=
>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D
>>>>Database: GenBank Updates (101.0+, 07/16/97)
>Query: "aa390074" [acc] OR "aa390074" [loc]
>Parse status: OK: 0 documents retrieved.
>//
>Database: GenBank (101.0, 6/14/97)
>Query: "aa390074" [acc] OR "aa390074" [loc]
>Parse status: OK: 1 document retrieved.
>Documents selected: 1-1 (up to 1000 lines)
>>LOCUS AA390074 393 bp mRNA EST =
23-APR-1997
>DEFINITION vb44f12.r1 Soares mouse lymph node NbMLN Mus musculus =
cDNA clone
> 751823 5'.
>ACCESSION AA390074
>NID g2043028
>KEYWORDS EST.
>SOURCE house mouse.
> ORGANISM Mus musculus
> Eukaryotae; mitochondrial eukaryotes; Metazoa; =
Chordata;
> Vertebrata; Mammalia; Eutheria; Rodentia; =
Sciurognathi; Muridae;
> Murinae; Mus.
>REFERENCE 1 (bases 1 to 393)
> AUTHORS Marra,M., Hillier,L., Allen,M., Bowles,M., =
Dietrich,N., Dubuque,T.,
> Geisel,S., Kucaba,T., Lacy,M., Le,M., Martin,J., =
Morris,M.,
> Schellenberg,K., Steptoe,M., Tan,F., Underwood,K., =
Moore,B.,
> Theising,B., Wylie,T., Lennon,G., Soares,B., =
Wilson,R. and
> Waterston,R.
> TITLE The WashU-HHMI Mouse EST Project
> JOURNAL Unpublished (1996)
>COMMENT
>> Contact: Marra M/Mouse EST Project
> WashU-HHMI Mouse EST Project
> Washington University School of MedicineP
> 4444 Forest Park Parkway, Box 8501, St. Louis, MO =
63108
> Tel: 314 286 1800
> Fax: 314 286 1810
> Email: mouseest at watson.wustl.edu> This clone is available royalty-free through LLNL ; =
contact the
> IMAGE Consortium (info at image.llnl.gov) for further =
information.
> MGI:460807
> Seq primer: -28m13 rev2 ET from Amersham
> High quality sequence stop: 324.
>FEATURES Location/Qualifiers
> source 1..393
> /organism=3D"Mus musculus"
> /strain=3D"C57BL/6J"
> /note=3D"Vector: pT7T3D-Pac (Pharmacia) with =
a modified
> polylinker; Site_1: Not I; Site_2: Eco RI; =
1st strand cDNA
> was primed with a Not I - oligo(dT) primer =
[5'
> =
TGTTACCAATCTGAAGTGGGAGCGGCCGCGATACTTTTTTTTTTTTTTTTTTTTTTTT
> 3']; double-stranded cDNA was ligated to Eco =
RI adaptors
> (Pharmacia), digested with Not I and cloned =
into the Not I
> and Eco RI sites of the modified pT7T3 =
vector. RNA
> provided by Dr. Bertrand Jordan. Library =
constructed and
> normalized by Bento Soares and M.Fatima =
Bonaldo."
> /clone=3D"751823"
> /clone_lib=3D"Soares mouse lymph node NbMLN"
> /sex=3D"male"
> /dev_stage=3D"4 weeks"
> /lab_host=3D"DH10B"
> mRNA <1..>393
>BASE COUNT 144 a 63 c 70 g 116 t
>ORIGIN
> 1 acattgaatt catatgttct caccttttta aaaatttcca tacaacttga =
gaattaggta
> 61 agttcctttg tatacaaatt tcagcagcta ggatatgtca cccttcagta =
ctacaaagta
> 121 cagaaattcc tagaatataa tcattctcac agaatagata ccaagaaaaa =
gctatctatt
> 181 aggtttctaa ttccaggacc tagatagaca agtacacttt taattgaggc =
caaatgatga
> 241 gccacaatgg taacccataa ctaaatagag gacaaagaac ataagtatga =
tgcaaaatga
> 301 gaggtaggat gtgtagcagg attccaaatt ttagcttaat tgtctttgac =
aatggactat
> 361 ttggagaaat gaatgaatag gttgtggctg tca
>//
>botka at socrates.8% more aa390074.gb_est11
LOCUS AA390074 393 bp mRNA EST =
23-APR-1997
DEFINITION vb44f12.r1 Soares mouse lymph node NbMLN Mus musculus =
cDNA clone
751823 5'.
ACCESSION AA390074
NID g2043028
KEYWORDS EST.
SOURCE house mouse.
ORGANISM Mus musculus
Eukaryotae; mitochondrial eukaryotes; Metazoa; =
Chordata;
Vertebrata; Mammalia; Eutheria; Rodentia; =
Sciurognathi; Muridae;
Murinae; Mus.
REFERENCE 1 (bases 1 to 393)
AUTHORS Marra,M., Hillier,L., Allen,M., Bowles,M., =
Dietrich,N., Dubuque,T.,
Geisel,S., Kucaba,T., Lacy,M., Le,M., Martin,J., =
Morris,M.,
Schellenberg,K., Steptoe,M., Tan,F., Underwood,K., =
Moore,B.,
Theising,B., Wylie,T., Lennon,G., Soares,B., Wilson,R. =
and
Waterston,R.
TITLE The WashU-HHMI Mouse EST Project
JOURNAL Unpublished (1996)
COMMENT
Contact: Marra M/Mouse EST Project
WashU-HHMI Mouse EST Project
Washington University School of MedicineP
4444 Forest Park Parkway, Box 8501, St. Louis, MO =
63108
Tel: 314 286 1800
Fax: 314 286 1810
Email: mouseest at watson.wustl.edu
This clone is available royalty-free through LLNL ; =
contact the
IMAGE Consortium (info at image.llnl.gov) for further =
information.
MGI:460807
Seq primer: -28m13 rev2 ET from Amersham
High quality sequence stop: 324.
FEATURES Location/Qualifiers
source 1. .393
/organism=3D"Mus musculus"
/strain=3D"C57BL/6J"
/note=3D"Vector: pT7T3D-Pac (Pharmacia) with =
a modified
polylinker; Site_1: Not I; Site_2: Eco RI; =
1st strand cDNA
was primed with a Not I - oligo(dT) primer =
[5'
=
TGTTACCAATCTGAAGTGGGAGCGGCCGCGATACTTTTTTTTTTTTTTTTTTTTTTTT
3']; double-stranded cDNA was ligated to Eco =
RI adaptors
(Pharmacia), digested with Not I and cloned =
into the Not I
and Eco RI sites of the modified pT7T3 =
vector. RNA
provided by Dr. Bertrand Jordan. Library =
constructed and
normalized by Bento Soares and M.Fatima =
Bonaldo."
/clone=3D"751823"
/clone_lib=3D"Soares mouse lymph node NbMLN"
/sex=3D"male"
/dev_stage=3D"4 weeks"
/lab_host=3D"DH10B"
mRNA <1. .>393
BASE COUNT 144 a 63 c 70 g 116 t
ORIGIN
AA390074 Length: 393 July 16, 1997 17:19 Type: N Check: 6583 =
..
1 TCCTTCCTTC CTTCTGTCTG TCCTTCTGTC CTTCCTTCCT TCTGTCTGTT=20=
51 TCTCTGTCTG TCCGTCTGTC CTTCTGTTTC TTTCTTTCTC CGTTTCTCCG=20=
101 TCCGTTTCTC TGTTTCTCCT TCCGTTTCTC CTTCCGTTTC TCTGTCTGTT=20=
151 TCTCCGTCCG TCCTTTTCTC CTTTTCTTTC TTTCTTTCTT TCTCCTTCCT=20=
201 TCCTTTTCTC TGTCCTTTTC TCTGTTTCTT TCTTTCTCTG CCAATTTCTT=20=
251 TCTCCGTCCT TCCTTTTCTC CTTTTCTCCT CCAACGGATA TGTAATTGGC=20=
301 CGCACGCCCG CGCGTGCGTC CGATCGTGTG GCTATGTACA TGGCTCCTTC=20=
351 CTCGCGCGAC CGTTCGCTCG TTCGACTGGC TCCTTCCTCG CGC
______
Christopher W Botka Phone: (415)476-5379
Sequence Analysis Consulting Service Fax: (415)502-1755
UCSF Computer Graphics Lab Office: Lib-111
Internet: botka at cgl.ucsf.edu Mail Drop: Bx 0446
http://www.cgl.ucsf.edu/sacs/ NeXT/MIME mail OK
