title: A comparative guide to gene prediction tools for the bioinformatics amateur.
abstract: Several hundred programs using different algorithms have been designed to predict individual coding features within any genomic sequence, but none of these tools covers all aspects of a gene or is 100% accurate in its prediction. Automated simultaneous processing of the results from a number of these programs minimizes the chance of a false positive prediction and quickly generates integrated data. We report here on the analysis of two known genes in 5 and 25 kb segments of genomic sequence using four genome annotation packages, NIX, RUMMAGE, Genotator and EMBOSS. Gene predictions were confirmed using cDNA sequences and a comparison was made between the packages. This study showed a similarity in the ability of NIX, RUMMAGE and Genotator to predict well-characterised genes and basic structures, but poor exon prediction for a small, 3 exon gene. However, the BLAST subprograms of all three packages correctly identified the 3 exons. In addition, EST BLAST subprograms identified a previously undescribed, possible 5' untranslated exon for the smaller gene and a number of putative alternatively spliced exons in the larger gene. Overall, NIX was found to be the most user-friendly package, in terms of easy access to databases and the interactive graphical display of results.
authors.affiliation: Molecular Genetics and Oncology Group, Clinical Dental Sciences, University of Liverpool, Liverpool, L69 3GN, UK.
authors.forename: J
authors.initials: J
authors.lastname: Jones
authors.forename: J K
authors.initials: JK
authors.lastname: Field
authors.forename: J M
authors.initials: JM
authors.lastname: Risk
mesh_terms: D000465:Algorithms; D002886:Chromosomes, Human, Pair 17 / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000235:genetics*; D018076:DNA, Complementary / Q000235:genetics; D016208:Databases, Factual; D020224:Expressed Sequence Tags; D015870:Gene Expression / Q000235:genetics*; D006801:Humans; D009687:Nuclear Proteins / Q000235:genetics*; D012326:RNA Splicing; D012261:Ribonucleoproteins / Q000235:genetics; D000068103:Serine-Arginine Splicing Factors; D012799:Sialyltransferases / Q000235:genetics*; D012984:Software; D017381:Spliceosomes
chemical_list: D018076:DNA, Complementary; D009687:Nuclear Proteins; D012261:Ribonucleoproteins; C073288:SRSF2 protein, human; D000068103:Serine-Arginine Splicing Factors; D004247:DNA; D012799:Sialyltransferases; C088391:galactosyl-1-3-N-acetylgalactosaminyl-specific 2,6-sialyltransferase