[PDF] Top 20 Prediction of RNA Secondary Structure from Random Sequences using ZEM
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Prediction of RNA Secondary Structure from Random Sequences using ZEM
... accurate structure prediction ...stable structure because of the presence of many interior loops and hairpins which are energetically ...the structure. ZEM Algorithm was therefore used ... See full document
5
Random generation of RNA secondary structures according to native distributions
... existing random generation algorithms for RNA secondary structures are used for predicting the structure of a given RNA sequence (see ...evaluating structure comparison softwares ... See full document
46
Novel polybasic cleavage site in SARS-CoV-2 genome is likely to induce a major change in the RNA secondary structure
... sequences include different variants with alterations in the 12-base motif CCUCGGCGGGCA [nucleotide positions 23603 – 23614]. Mutant DM lacks the 12-base motif, and other mutants include variations to alter the ... See full document
12
SP fold – Speculative Parallelization for Parallel Algorithm of RNA Secondary Structure Prediction on Multicore
... of RNA secondary structure prediction by Speculative Parallelization for modern multi-core computers is ...implemented using carefully tuned data structures, proper selection of ... See full document
5
ERV3 and Related Sequences in Humans: Structure and RNA Expression
... LTRs. Using ConSite at moderate stringency (10 bits), we determined that TFBS with more than one predicted occurrence in the 5 ⬘ LTR included 12 SOX-5, 5 HFH-2, 4 ROR ␣ 1, 3 Sox17, and 3 Thing1/E47 ...control ... See full document
15
Research on folding diversity in statistical learning methods for RNA secondary structure prediction
... different sequences, but they belong to an RNA structure set[2, 6, ...selected from the seed sequences of 22 RNA families ...the sequences of the two are completely ... See full document
11
A Phylogenetically Conserved Stem-Loop Structure at the 5′ Border of the Internal Ribosome Entry Site of Hepatitis C Virus Is Required for Cap-Independent Viral Translation
... conserved secondary RNA ...the structure of domain II of the 59NTR of HCV, a segment of the 59NTR which is known to contribute to IRES function ...dicted structure (9) and the previous ... See full document
10
Serology-Enabled Discovery of Genetically Diverse Hepaciviruses in a New Host
... pathogenesis using tractable animal ...expressed from the helicase domain of CHV NS3 was used as antigen in the luciferase immu- noprecipitation system (LIPS) assay to screen several nonprimate animal ... See full document
8
GTfold: Enabling parallel RNA secondary structure prediction on multi core desktops
... nearly indistinguishable distributions of accuracy. Each program has an average of only ∼ 40% for the 223 16S ribosomal sequences and the 55 23S ones. Given the high variance within programs (from a low of ... See full document
6
Accelerating calculations of RNA secondary structure partition functions using GPUs
... GPUs using CUDA, in many cases yielding speed-ups of several orders of magnitude ...for RNA sec- ondary structure ...of structure prediction by free energy minimization ...short ... See full document
8
RNA motif discovery: a computational overview
... ondary structure based local patterns from a set of related RNA ...input sequences. The set of input sequences for example could correspond to the 5 or 3 untranslated regions (UTR) of a ... See full document
22
Reconstructing phylogeny from RNA secondary structure via simulated evolution
... three-dimensional structure could in principle be determined from the sequence data alone, and considerable effort has been devoted to this endeavor 7,16–18,33 ... See full document
11
Secondary Structure of the Mature Ex Virio Moloney Murine Leukemia Virus Genomic RNA Dimerization Domain
... the structure be- tween PAL1 and PAL2 is different in the two RNAs and that this region forms the SL0 stem-loop only in the genomic RNA (structural differences between the ex virio and in vitro dimers are ... See full document
9
Bioinformatics analysis of metallothionein gene from Agaricus bisporus, Ganoderma lucidum, Taiwanofungus camphorates and Paxillus involutus
... detected from 4 MT gene sequences by the genetic diver- sity analysis of DnaSP (version ...tion using the total number of mutations, there was no significance (P > ... See full document
5
Protein secondary structure prediction from amino acid sequence using artificial intelligence technique
... Barton,1993) Sequences are rejected if their SCANPS probability score is higher than 1x10 -4 .... Sequences are also rejected if they do not fit a length cut-off of ...If sequences exceed the length ... See full document
264
Secondary Structure Prediction of Proteins Using Recurrent Nets-A Review
... series prediction with short sequences, though LSTM´s strength is “to learn to remember single events for very long, unknown time periods” [3] and could possibly be an advantage when training long ... See full document
5
Detection of vesicular stomatitis virus RNA and its defective-interfering particles in individual mouse brains.
... For differentiation of hybridizable sequences found in the RNA of DI particles from complementary or identical sequences in the L mRNA or standard genomic RNA of VSV, RNA obtained from m[r] ... See full document
6
Protein Secondary Structure Prediction using Pattern Recognition Neural Network
... protein structure by X-ray crystallography, a crystal structure determination may still require many ...protein structure, but NMR is also costly, time-consuming, requires large amounts of protein of ... See full document
6
CHARACTERIZATION OF ENDOGLIN GENE USING IN SILICO TOOLS
... CONCLUSION: Endoglin is a homodimeric membrane glycoprotein primarily associated with human vascular endothelium. The regulation through the polyol pathway is thought to affect the accumulation of endoglin that is ... See full document
6
An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding
... gies—Valiant, Four-Russians, and Sparsification—have been applied to speedup RNA secondary structure prediction. The sparsification method exploits two properties of the input: the number of ... See full document
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