Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications
Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications
Verbumculus and the discovery of unusual words
Journal of Computer Science and Technology - Special issue on bioinformatics
Clustal W and Clustal X version 2.0
Bioinformatics
Mining Loosely Structured Motifs from Biological Data
IEEE Transactions on Knowledge and Data Engineering
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IP6 Kinases (IP6Ks) are important mammalian enzymes involved in inositol phosphates metabolism. Although IP6Ks have not yet been identified in plant chromosomes, there are many clues suggesting that the corresponding gene might be found in plant mtDNA, encrypted and hidden by virtue of editing and/or trans-splicing processes. In this paper, we propose an approach to search for the gene IP6K and applied it on mitocondrial DNA (mtDNA) of plants. To search for the gene IP6K, we applied a technique based on motif discovery by considering the nucleotide sequence corresponding to a specific tag of the IP6K family. Such a tag has been found in all IP6K genes identified up to now, as well as in all genes belonging to the Inositol Polyphosphates Kinases (IPK) superfamily. IPK tag sequence corresponds to the catalytic site of the enzyme and it can be considered as an identifier of IPK genes. The analysis we conducted provided the relevant negative answer that IP6K does not actually occur in vegetable mtDNA. Finally, we also validated our approach by searching for the known Ipk1 gene in Arabidopsis thaliana genome.