Searching for RNA genes using base-composition statistics

• Published in: Nucleic acids research 2002-05, Vol.30 (9), p.2076-2082
• Main Author: Schattner, Peter
• Format: Article
• Language: English
• Subjects: Animals; Base Composition; Base Sequence; Caenorhabditis elegans - genetics; Feasibility Studies; GC Rich Sequence; Genetic Variation; Genome; Methanococcus - genetics; Methanococcus jannaschii; Models, Statistical; Molecular Sequence Data; Plasmodium falciparum - genetics; ribonuclease P; RNA, Ribosomal - genetics; RNA, Transfer - genetics; RNA, Untranslated - genetics; Sequence Alignment; signal recognition particle
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/30.9.2076

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.