Search results
Results from the WOW.Com Content Network
Predict the minimum free energy structure of nucleic acids. seqfold is an implementation of the Zuker, 1981 dynamic programming algorithm, the basis for UNAFold/mfold, with energy functions from SantaLucia, 2004 (DNA) and Turner, 2009 (RNA). MIT license. Python CLI or module. No: link & source [30] Sfold: Statistical sampling of all possible ...
Thus, popular secondary structure prediction methods like Mfold and Pfold will not predict pseudoknot structures present in a query sequence; they will only identify the more stable of the two pseudoknot stems.
Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences.
Software for thermodynamic modeling of nucleic acids includes Nupack, [6] [7] mfold/UNAFold, [8] and Vienna. [9] A related approach, inverse secondary structure prediction, uses stochastic local search which improves a nucleic acid sequence by running a structure prediction algorithm and the modifying the sequence to eliminate unwanted features ...
Below is a figure produced by mfold [20] showing predicted mRNA structure of the 3' UTR of C1orf185. Possible mRNA secondary structure of C1orf185 made by mfold. [20] There are 3 main branches that end in 1-2 stem loops each. The stem loop near the end of the sequence contains the Poly-A signal, which signals the end of transcription.
Many eukaryotic cells contain large ribonucleoprotein particles in the cytoplasm known as vaults. [3] The vault complex comprises the major vault protein (), two minor vault proteins (VPARP and TEP1), and a variety of small untranslated RNA molecules known as vault RNAs (vRNAs, vtRNAs) only found in higher eukaryotes.
The Nussinov algorithm does not account for the three-dimensional shape of RNA, nor predict RNA pseudoknots. [2] Furthermore, in its basic form, it does not account for a minimum stem loop size.
The cleavage site of leadzyme is located within a four-nucleotide long asymmetric internal loop that also consists of RNA helices on its both sides. This is shown in top figure on right, which is the secondary structure of leadzyme generated using mfold. The structures of leadzyme have also been solved using X-ray crystallography and NMR.