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Publications for RNAProfile
RNA motif discovery: a computational overview
[…] ee occurs as a sub-graph of the data tree in the sense that if node b is a child of node a in the pattern tree, then the node in the data tree associated with node b need to only be a descendant of a.RNAProfile  is a relatively simple method with a heuristic approach. The approach in principle is very similar to the initialization step of CMfinder to build the initial alignments. It also takes a […]
Classification and assessment tools for structural motif discovery algorithms
[…] cover structural motifs in more than two input sequences, where the input sequences are different, but share a common RNA structure. Among the surveyed tools, we were able to obtain six: CMfinder , RNAProfile , RNAmine , comRNA , RNAPromo , and Seed . Our first observation is that the use of structural discovery tools often requires knowledge of the Unix operating system. Except for RN […]
A computational method to predict genetically encoded rare amino acids in proteins
[…] ted ORFs passing the previous tests in each bacterial organism. The extracted set of RNA sequences for each organism was used to detect a common, single hairpin motif using the rapid, heuristic-based RNAPROFILE program . A test calculation predicted the known SECIS element of the gene encoding FDH from E. coli correctly  (Figure ). The putative SECIS hairpin motifs were manually inspected for […]
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