To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistently low false-negative rate. The incorporation of similarity information is meant to reduce the false-positive rate, but in doing so it increases the false-negative rate. The crucial variable is gene size (including introns) — genes of the most extreme sizes, especially very large genes, are most likely to be incorrectly predicted.
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We thank E. Eyras at the Sanger Center, UK, for explaining the details of the Ensembl procedures to us. This work was sponsored by the Chinese Academy of Sciences, Commission for Economy Planning, Ministry of Science and Technology, National Natural Science Foundation of China, Beijing Municipal Government, Zhejiang Provincial Government and Hangzhou Municipal Government. Some of this work was also supported by the National Human Genome Research Institute.
- AB INITIO GENE PREDICTION
The identification of protein-coding genes in genomic sequence, using no prior knowledge other than the signal and content terms.
An almond-shaped neurostructure that is involved in the production and response to non-verbal signs of anger, avoidance, defensiveness and fear.
- ANNOTATION PIPELINES
A series of computer procedures that is used to identify the biological contents of a sequenced genome. Gene finding is only the first of many steps. Subsequent steps might include the identification of homologous genes, the assignment of biological function and so on.
- CDS SIZE
The size of the spliced transcript, excluding introns. As gene-prediction programs do not detect untranslated regions, we do not include them in this definition.
- COMPLETE MISS
(CM). The probability that less than 100 bp of the protein-coding sequence of a gene is correctly predicted.
- CONTENT TERMS
Patterns of codon usage, which are unique to each species, that allow protein-coding sequences to be distinguished from surrounding non-coding sequence.
- FALSE DESERT
(FD). A fraction of a sequence of a gene, including its introns which is not covered by any of the gene predictions.
- FALSE NEGATIVE
(FN). The probability that a segment that is known to code for protein is not correctly predicted to be coding, specified as a per-base pair or per-amino acid rate.
- FALSE POSITIVE
(FP). The probability that a segment that is predicted to code for protein is not in fact known to be coding, given as a per-base pair or per-amino acid rate. Note that we only count those exons that have some overlap to the region of the genome that is defined by the cDNA alignment. Exons that lie outside this region are relegated to the over-predictions.
- GENE SIZE
The size of the unspliced transcript, including introns. As gene-prediction programs do not detect untranslated regions, we do not include them in this definition.
- OUTLIER GENES
Genes the sequence characteristics of which are sufficiently outside the normal range to create problems for ab initio gene prediction.
Predicted exons that lie entirely outside the region of the genome that is defined by the complementary DNA alignment, but which are part of a prediction that has some overlap with this region. Note the distinction between this and false positives.
- PER-AMINO ACID RATE
(Per-aa rate). In computing FPs and FNs, this is the method in which we also insist that the correct amino acids are predicted, which requires that the reading frame is correctly assigned.
- PER-BASE PAIR RATE
(Per-bp rate). In computing FPs and FNs, this is the method in which we only ask that the correct nucleotides are predicted, without checking if the reading frame is correctly assigned.
The division of GenBank that is devoted to full-length reference sequences for experimentally confirmed genes.
A measure of prediction that is equivalent to one minus the false-negative rate.
- SERIAL ANALYSIS OF GENE EXPRESSION
(SAGE). A quantitative expression assay that is based on tags that are 10–20 bp in length, which are derived from mRNAs.
- SIGNAL TERMS
Short sequence motifs, such as splice sites, branch points, polypyrimidine tracts, start codons and stop codons, that are used to detect exon boundaries.
A measure of prediction that is equivalent to one minus the false-positive rate.
- TRAINING SET
A set of known protein-coding sequences that is used to teach the ab initio gene-prediction program what the codon-usage patterns look like for a given species.
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Wang, J., Li, S., Zhang, Y. et al. Vertebrate gene predictions and the problem of large genes. Nat Rev Genet 4, 741–749 (2003). https://doi.org/10.1038/nrg1160
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