An approach for the identification of microRNA with an application to Anopheles gambiae.
MicroRNAs (miRNAs) are an abundant class of 20-27 nt long noncoding RNAs, involved in post-transcriptional regulation of genes in eukaryotes. These miRNAs are usually highly conserved between the genomes of related organisms and their pre-miRNA transcript, about 60-120 nt long, forms extended stem-loop structure. Keeping these facts in mind miRsearch is developed which relies on searching the homologues of all known miRNAs of one organism in the genome of a related organism allowing few mismatches depending on the phylogenetic distance between them, followed by assessing for the capability of formation of stem-loop structure. The precursor sequences so obtained were then screened through the RNA folding program MFOLD selecting the cut-off values on the basis of known Drosophila melanogaster pre-miRNAs. With this approach, about 91 probable candidate miRNAs along with pre-miRNAs were identified in Anopheles gambiae using known D. melanogaster miRNAs. Out of these, 41 probable miRNAs have 100% similarity with already known D. melanogaster miRNAs and others were found to be at least 85% similar to the miRNAs of various other organisms.
Chatterjee
Raghunath
R
Human Genetics & Genomics Group, Indian Institute of Chemical Biology, Jadavpur, Kolkata, India.
Chaudhuri
Keya
K
D000818:Animals; D000852:Anopheles / Q000235:genetics*; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics*; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA / Q000379:methods
D035683:MicroRNAs