Searching for RNA genes using base-composition statistics.
The hypothesis that genomic regions rich in non-protein-coding RNAs (ncRNAs) can be identified using local variations in single-base and dinucleotide statistics has been investigated. (G+C)%, (G-C)% difference, (A-T)% difference and dinucleotide-frequency statistics were compared among seven classes of ncRNAs and three genomes. Significant variations were observed in (G+C)% and, in Methanococcus jannaschii, in the frequency of the dinucleotide 'CG'. Screening programs based on these two base-composition statistics were developed. With (G+C)% screening alone, a 1% fraction of the M.jannaschii genome containing all 44 known transfer RNAs, ribosomal RNAs and signal recognition particle RNAs could be identified. When (G+C)% combined with CG dinucleotide-frequency screening was used, 43 of the 44 known M.jannaschii structural ncRNAs were again identified, while the number of presumably false hits overlapping a known or putative protein-coding gene was reduced from 15 to 6. In addition, 19 candidate ncRNAs were identified including one with significant homology to several known archaeal RNaseP RNAs.
Schattner
Peter
P
Center for Biomolecular Science and Engineering, 227 Sinsheimer Laboratories, University of California, 1156 High Street, Santa Cruz, CA 95064, USA. schattner@cse.ucsc.edu
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D005240:Feasibility Studies; D020862:GC Rich Sequence; D014644:Genetic Variation; D016678:Genome; D017017:Methanococcus / Q000235:genetics; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010963:Plasmodium falciparum / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D016415:Sequence Alignment
D012335:RNA, Ribosomal; D022661:RNA, Untranslated; D012343:RNA, Transfer