Search Results for "secondary structure" - Page 2

ViNSS View is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. ViNSS View allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, ViNSS View allows you to incorporate non-canonical base pairs into your drawing.

AlignMe is a C++ program to align distantly related membrane proteins by including several input parameters. Alignments based on substitution matrices, Position Specific Matrices (PSSMs), hydrophobicity scales and any kind of profiles (membrane predictions, secondary structure predictions etc.).

BoulderALE is an RNA alignment editor, which allows for the annotation of basepairs, annotation and collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences and base composition given a secondary structure.

The sibRNAfold program is a modification of the Vienna RNAfold program for RNA secondary structure prediction through energy minimization.

Here we describe the algorithm RNAborMEA, which for an arbitrary initial structure S0 and for all values 0 < k < n, computes the secondary structure MEA(k), having maximum expected accuracy over all k-neighbors of S0.

YaSeTo implements a modification of the widely used Sankoff-Algorithm for sequence/structure alignments of RNA sequences. It is suitable for genome-wide ncRNA gene finding, in case the ncRNA exhibits a conserved secondary structure.

Utility programme to calculate Paired-Unpaired change ratio of RNA secondary structure

DANGLE: A Bayesian inferential prediction method for protein backbone dihedral angles and secondary structure assignments, solely from sequence information, experimental chemical shifts and a database of known protein structures and their shifts.

NEP is a network management software platform based on Netconf protocol. It implements all the basic functions of Netconf. Also, it is hithly scalable and the program structure allows users to conveniently carry out the secondary development.

A visualization and design tool for RNA secondary structure

ProteinArchitect facilitates the visual exploration of the architecture of proteins, including conserved domains, secondary structure elements and structurally flexible regions, e.g. in the context of the analysis of protein superfamilies.