A method to identify the non-coding RNA gene for U1 RNA in species in which it has not yet been found

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BackgroundNon coding RNAs are the RNA molecules that do not code for proteins but play structural, catalytic or regulatory roles in the organisms in which they are found. These RNAs generally conserve their secondary structure more than their primary sequence. It is possible to look for protein coding genes using sequence signals like promoters, terminators, start and stop codons etc. However, this is not the case with non coding RNAs since these signals are weakly conserved in them. Hence the situation with non coding RNAs is more challenging. Therefore a protocol is devised to identify U1 RNA in species not previously known to have it.ResultsIt is sufficient to use the covariance models to identify non coding RNAs but they are very slow and hence a filtering step is needed before using the covariance models to reduce the search space for identifying these genes. The protocol for identifying U1 RNA genes employs for the filtering a pattern matcher RNABOB that can conduct secondary structure pattern searches. The descriptor for RNABOB is made automatically such that it can also represent the bulges and interior loops in helices of RNA. The protocol is compared with the Rfam and Weinberg & Ruzzo approaches and has been able to identify new U1 RNA homologues in the Apicomplexan group where it has not previously been found.ConclusionsThe method has been used to identify the gene for U1 RNA in certain species in...