ArticleNucleic acids research1996
Cleaning the GenBank Arabidopsis thaliana data set.
Article in Nucleic acids research, 1996. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases.Genomics, proteomics & bioinformatics · 2020Article
- Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR).Microbial genomics · 2018Article
- Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.Database : the journal of biological databases and curation · 2017Article
- Article
- DNA barcoding insect-host plant associations.Proceedings. Biological sciences · 2009Article
- An optimized procedure greatly improves EST vector contamination removal.BMC genomics · 2007Article
- Impact of RNA structure on the prediction of donor and acceptor splice sites.BMC bioinformatics · 2006Article
- Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA.Nucleic acids research · 2004Article
- EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences.Nucleic acids research · 2003Article
- The maize genome contains a helitron insertion.The Plant cell · 2003Article
- A splice site mutant of maize activates cryptic splice sites, elicits intron inclusion and exon exclusion, and permits branch point elucidation.Plant physiology · 1999Article
- Identification of protein-coding regions in Arabidopsis thaliana genome based on quadratic discriminant analysis.Plant molecular biology · 1998Article
- A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites.Nucleic acids research · 1997Article
- Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences.Nucleic acids research · 1996Article
- Sequence analysis of an 81 kb contig from Arabidopsis thaliana chromosome III.Nucleic acids research · 1996Article
- Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks.Protein science : a publication of the Protein Society · 1996Article
- Splicing of precursors to mRNA in higher plants: mechanism, regulation and sub-nuclear organisation of the spliceosomal machinery.Plant molecular biology · 1996Review
- Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information.Nucleic acids research · 1996Article
Corrections and comments
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
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.
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