ArticleNucleic acids research1994
Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.
Article in Nucleic acids research, 1994. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
59 citing papers in PubMed, 362 citations in OpenAlex.
- Identification of an elusive spliceogenic MYBPC3 variant in an otherwise genotype-negative hypertrophic cardiomyopathy pedigree.Scientific reports · 2022Article
- LEMONS - A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes.PloS one · 2015Article
- The structure and retrotransposition mechanism of LTR-retrotransposons in the asexual yeast Candida albicans.Virulence · 2014Review
- Evolutionary relationship and structural characterization of the EPF/EPFL gene family.PloS one · 2013Article
- POLYAR, a new computer program for prediction of poly(A) sites in human sequences.BMC genomics · 2010Article
- Comparison of the chloroplast peroxidase system in the chlorophyte Chlamydomonas reinhardtii, the bryophyte Physcomitrella patens, the lycophyte Selaginella moellendorffii and the seed plant Arabidopsis thaliana.BMC plant biology · 2010Article
- hnRNP A1 and hnRNP H can collaborate to modulate 5' splice site selection.RNA (New York, N.Y.) · 2010Article
- Peptide vocabulary analysis reveals ultra-conservation and homonymity in protein sequences.Bioinformatics and biology insights · 2009Article
- Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains.BMC genomics · 2008Article
- Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae.Genetics · 2008Article
- Multi-scale parametric spectral analysis for exon detection in DNA sequences based on forward-backward linear prediction and singular value decomposition of the double-base curves.Bioinformation · 2008Article
- Engineering infectious cDNAs of coronavirus as bacterial artificial chromosomes.Methods in molecular biology (Clifton, N.J.) · 2008Article
- Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.BMC bioinformatics · 2007Article
- Identification and comparative analysis of novel alternatively spliced transcripts of RhoGEF domain encoding gene in C. elegans and C. briggsae.Bioinformation · 2007Article
- Comparative analysis of various gene finders specific to Caenorhabditis elegans genome.Bioinformation · 2006Article
- Intronic binding sites for hnRNP A/B and hnRNP F/H proteins stimulate pre-mRNA splicing.PLoS biology · 2006Article
- Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae.Genome research · 2005Article
- A brief review of computational gene prediction methods.Genomics, proteomics & bioinformatics · 2004Review
- Fragile site orthologs FHIT/FRA3B and Fhit/Fra14A2: evolutionarily conserved but highly recombinogenic.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- A novel approach to describe a U1 snRNA binding site.Nucleic acids research · 2003Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A new method which predicts internal exon sequences in human DNA has been developed. The method is based on a splice site prediction algorithm that uses the linear discriminant function to combine information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotides in protein coding and intron regions. The accuracy of our splice site recognition function is 97% for donor splice sites and 96% for acceptor splice sites. For exon prediction, we combine in a discriminant function the characteristics describing the 5'-intron region, donor splice site, coding region, acceptor splice site and 3'-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79%. The recognition quality computed at the level of individual nucleotides is 89% for exon sequences and 98% for intron sequences. This corresponds to a correlation coefficient for exon prediction of 0.87. The precision of this approach is better than other methods and has been tested on a larger data set. We have also developed a means for predicting exon-exon junctions in cDNA sequences, which can be useful for selecting optimal PCR primers.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.