Ab initio gene finding in Drosophila genomic DNA.

By A. Salamov, Victor V. Solovyev. Genome Research, 2000

1,212 citations recorded by the source corpus.

Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained using (human gene predictor) and Fgenesh programs that have organism-specific parameters for human, Drosophila, plants, yeast, and nematode. We did not use information about cDNA/EST in most predictions to model a real situation for finding new genes because information about complete cDNA is often absent or based on very small partial fragments. We investigated the accuracy of gene prediction on different levels and designed several schemes to predict an unambiguous set of genes (annotation CGG1), a set of reliable exons (annotation CGG2), and the most complete set of exons (annotation CGG3). For 49 genes, protein products of which have clear homologs in protein databases, predictions were recomputed by Fgenesh+ program. The first annotation serves as the optimal computational description of new sequence to be presented in a database. Reliable exons from the second annotation serve as good candidates for selecting the PCR primers for experimental work for gene structure verification. Our results shows that we can identify approximately 90% of coding nucleotides with 20% false positives. At the exon level we accurately predicted 65% of exons and 89% including overlapping exons with 49% false positives. Optimizing accuracy of prediction, we designed a gene identification scheme using Fgenesh, which provided sensitivity (Sn) = 98% and specificity (Sp) = 86% at the base level, Sn = 81% (97% including overlapping exons) and Sp = 58% at the exon level and Sn = 72% and Sp = 39% at the gene level (estimating sensitivity on std1 set and specificity on std3 set). In general, these results showed that computational gene prediction can be a reliable tool for annotating new genomic sequences, giving accurate information on 90% of coding sequences with 14% false positives. However, exact gene prediction (especially at the gene level) needs additional improvement using gene prediction algorithms. The program was also tested for predicting genes of human Chromosome 22 (the last variant of Fgenesh can analyze the whole chromosome sequence). This analysis has demonstrated that the 88% of manually annotated exons in Chromosome 22 were among the ab initio predicted exons. The suite of gene identification programs is available through the WWW server of Computational Genomics Group at http://genomic.sanger.ac.uk/gf. html.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/eeffcc88f5738b09d571f9693f1c69468bbe967a

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Citations in the corpus

A candidate gene for fire blight resistance in Malus ×robusta 5 is coding for a CC–NBS–LRR (2013, methodology): “The ORFs were predicted using FGENESH with algorithms for tomato, Arabidopsis thaliana (dicot plants) and Vitis vinifera (Salamov and Solovyev 2000).”
MycoCosm portal: gearing up for 1000 fungal genomes (2013, background): “Homology-based Fgenesh+ (9) and Genewise Figure 3.”
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003, methodology): “Subsequently, four of the additional N-terminal exons that were predicted by FGENESH and Genefinder were confirmed by new EST data (marked with asterisks).”
GENCODE: producing a reference annotation for ENCODE (2006, methodology): “…by a panel of automated gene prediction algorithms before the E-GASP workshop (Geneid [12], Genescan [13], Twinscan [14], SGP [15], Fgenesh [16], Exonify [17], Acembly [18] Ecgene [19], Ensembl EST [20]) that lie outside a HAVANA annotated gene in 13 of the 44 ENCODE regions (corresponding…”
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments (2007, methodology): “The ab initio gene prediction programs Fgenesh [5], Gene-Mark.hmm [6], and GlimmerHMM [4] were applied to the rice genome sequences.”
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis (2013, methodology): “9 were predicted using FGENESH+ (22) and GeneWise (23) seeded by BLASTx alignments of genomic sequence against sequences from the NCBI non-redundant protein set nr and from the JGI Phycomyces and Mucor annotations (http://jgi.”
The Vertebrate Genome Annotation (Vega) database (2004, methodology): “We also run a number of ab initioprediction algorithms: genscan (26) and fgenesh (27) for genes, tRNAscan (28) to find tRNAgenes”