Home LiteratureArticle Details

PMID: 8628656 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Cleaning the GenBank Arabidopsis thaliana data set.

Nucleic acids research ·Vol. 24 ·No. 2 ·1996-01-15 ·Pages 316-20

Korning PG, Hebsgaard SM, Rouze P, Brunak S

Abstract

Data driven computational biology relies on the large quantities of genomic data stored in international sequence data banks. However, the possibilities are drastically impaired if the stored data is unreliable. During a project aiming to predict splice sites in the dicot Arabidopsis thaliana, we extracted a data set from the A.thaliana entries in GenBank. A number of simple 'sanity' checks, based on the nature of the data, revealed an alarmingly high error rate. More than 15% of the most important entries extracted did contain erroneous information. In addition, a number of entries had directly conflicting assignments of exons and introns, not stemming from alternative splicing. In a few cases the errors are due to mere typographical misprints, which may be corrected by comparison to the original papers, but errors caused by wrong assignments of splice sites from experimental data are the most common. It is proposed that the level of error correction should be increased and that gene structure sanity checks should be incorporated--also at the submitter level--to avoid or reduce the problem in the future. A non-redundant and error corrected subset of the data for A.thaliana is made available through anonymous FTP.

MeSH Terms

Algorithms Arabidopsis/genetics Base Sequence DNA, Plant/genetics Databases, Factual Genome, Plant Introns Molecular Sequence Data Neural Networks, Computer RNA Splicing/genetics

Chemicals

DNA, Plant

Authors & Affiliations

4 authors, click to expand affiliations / ORCID

Korning P G

Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark.

Hebsgaard S M

Rouze P

Brunak S

References (9)

9 references, click to expand

Neural network detects errors in the assignment of mRNA splice sites.
Nucleic Acids Res. 1990 Aug 25;18(16):4797-801 PMID: 2395643
Cleaning up gene databases.
Nature. 1990 Jan 11;343(6254):123 PMID: 2296305
Arabidopsis phosphoribosylanthranilate isomerase: molecular genetic analysis of triplicate tryptophan pathway genes.
Plant Cell. 1995 Apr;7(4):447-61 PMID: 7773017
Nucleotide and protein sequences of a cytoplasmic ribosomal protein S15a gene from Arabidopsis thaliana.
Plant Physiol. 1994 Sep;106(1):401-2 PMID: 7972526
The unusual 5' splicing border GC is used in myrosinase genes of the Brassicaceae.
Plant Mol Biol. 1995 Oct;29(1):167-71 PMID: 7579162
The minimum functional length of pre-mRNA introns in monocots and dicots.
Plant Mol Biol. 1990 May;14(5):727-33 PMID: 2102851
Prediction of human mRNA donor and acceptor sites from the DNA sequence.
J Mol Biol. 1991 Jul 5;220(1):49-65 PMID: 2067018
Database of homology-derived protein structures and the structural meaning of sequence alignment.
Proteins. 1991;9(1):56-68 PMID: 2017436
Selection of representative protein data sets.
Protein Sci. 1992 Mar;1(3):409-17 PMID: 1304348

Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

0305-1048

DOI

10.1093/nar/24.2.316

Published

1996-01-15

Pages

316-20

Language

English

Region

England

NLM ID

0411011

PMCID

PMC145627

Subset

Databases

GENBANK

D13044, L22568, L24119, L27461, M12196, M37247, M84343, M85253, M93023, U08315, U09339, U11033, U18969, X13708, X51474, X51799, X55970, X62281, X68146, X69376, X70990, X73839, X74515, X74734, X81799, X81800, Z12614, Z22958, Z31589, Z31715

External Links

PubMed source DOI: 10.1093/nar/24.2.316 PMC Full Text View journal details

Analysis Services

Cleaning the GenBank Arabidopsis thaliana data set.

Contact

WeChat Official Account