Long intergenic noncoding RNAs (lincRNAs) are known to be tissue specifically expressed and able to regulate functional protein-coding genes: some can even act as competing endogenous RNAs (ceRNAs), because microRNAs can bind to them instead of the corresponding mRNA binding sites. Some lincRNAs contain remnants of protein-coding sequences and it has been hypothesized that they might arise after a pseudogenization processes. However, a major limitation in the study of such phenomenon is the lack of proper computational tools designed to align/analyze protein-coding sequences and noncoding sequences. To overcome this limitation, we published a method that finds the remnants of protein-coding sequences within the sequence of lincRNAs, as well as the corresponding sequences in parental proteins. This method, together with the visualization platform for tracing frameshifts and single point mutations within this type of sequences, are described here.
Keywords: Protein homology; Protein-coding gene; Pseudogene; Rost curve; Sequence alignment; ceRNA; lincRNA gene; lncRNA gene; microRNA.