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. 2006;7 Suppl 1(Suppl 1):S10.1-12.
doi: 10.1186/gb-2006-7-s1-s10. Epub 2006 Aug 7.

Automatic annotation of eukaryotic genes, pseudogenes and promoters

Victor Solovyev  1 , Peter Kosarev, Igor Seledsov, Denis Vorobyev
Affiliations

Automatic annotation of eukaryotic genes, pseudogenes and promoters

Victor Solovyev et al. Genome Biol. 2006.

Abstract

Background: The ENCODE gene prediction workshop (EGASP) has been organized to evaluate how well state-of-the-art automatic gene finding methods are able to reproduce the manual and experimental gene annotation of the human genome. We have used Softberry gene finding software to predict genes, pseudogenes and promoters in 44 selected ENCODE sequences representing approximately 1% (30 Mb) of the human genome. Predictions of gene finding programs were evaluated in terms of their ability to reproduce the ENCODE-HAVANA annotation.

Results: The Fgenesh++ gene prediction pipeline can identify 91% of coding nucleotides with a specificity of 90%. Our automatic pseudogene finder (PSF program) found 90% of the manually annotated pseudogenes and some new ones. The Fprom promoter prediction program identifies 80% of TATA promoters sequences with one false positive prediction per 2,000 base-pairs (bp) and 50% of TATA-less promoters with one false positive prediction per 650 bp. It can be used to identify transcription start sites upstream of annotated coding parts of genes found by gene prediction software.

Conclusion: We review our software and underlying methods for identifying these three important structural and functional genome components and discuss the accuracy of predictions, recent advances and open problems in annotating genomic sequences. We have demonstrated that our methods can be effectively used for initial automatic annotation of the eukaryotic genome.

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Figures

Figure 1
Figure 1
Example of a processed pseudogene. Alignment versus protein encoded by the parent gene. Identity, 83.7%; coverage of protein sequence, 93.9%; number of internal stop codons, 2; number of frameshifts, I; Ka/Ks, 0.484.
Figure 2
Figure 2
Example of a pseudogene that has not been processed. Alignment versus protein encoded by the parent gene. Identity, 86.4%; coverage of protein sequence, 97.6%; number of internal stop codons, 3; number of frameshifts, 4; Ka/Ks, 0.594.
Figure 3
Figure 3
Pseudogene in ENm004 sequence, absent from HAVANA annotation. The alignment has a stop codon close to position 151636.
Figure 4
Figure 4
A distribution of predicted TSS relative to the start of mRNA sequences. Figures on the x-axis are centers of 100 bp intervals, for example, mark 50 corresponds to [+1,+100] interval.
Figure 5
Figure 5
A distribution of predicted TSS near the start of mRNA sequences. Figures on the x-axis are centers of 10 bp intervals, for example, mark 5 corresponds to [+1,+10] interval.
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