Global or local? Predicting secondary structure and accessibility in mRNAs
نویسندگان
چکیده
منابع مشابه
Global or local? Predicting secondary structure and accessibility in mRNAs
Determining the structural properties of mRNA is key to understanding vital post-transcriptional processes. As experimental data on mRNA structure are scarce, accurate structure prediction is required to characterize RNA regulatory mechanisms. Although various structure prediction approaches are available, it is often unclear which to choose and how to set their parameters. Furthermore, no stan...
متن کاملStatistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs
Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes for evolutionarily conserved secondary structure elements using RNA-Decoder, a comparative secondary structure prediction program that is capable of explicitly taking the known protein-coding contex...
متن کاملPredicting protein secondary structure and solvent accessibility with an improved multiple linear regression method.
We have improved the multiple linear regression (MLR) algorithm for protein secondary structure prediction by combining it with the evolutionary information provided by multiple sequence alignment of PSI-BLAST. On the CB513 dataset, the three states average overall per-residue accuracy, Q(3), reached 76.4%, while segment overlap accuracy, SOV99, reached 73.2%, using a rigorous jackknife procedu...
متن کاملOn predicting secondary structure transition
A function of a protein is dependent on its structure; therefore, predicting a protein structure from an amino acid sequence is an active area of research. To improve the accuracy of validation of structures, we are studying the predictability of secondary structure transitions using the following machine learning algorithms: naive Bayes, C4.5 decision tree, and random forest. The annotated dat...
متن کاملLocal Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites
The initiation of translation is a fundamental and highly regulated process in gene expression. Translation initiation in prokaryotic systems usually requires interaction between the ribosome and an mRNA sequence upstream of the initiation codon, the so-called ribosome-binding site (Shine-Dalgarno sequence). However, a large number of genes do not possess Shine-Dalgarno sequences, and it is unk...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2012
ISSN: 1362-4962,0305-1048
DOI: 10.1093/nar/gks181