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Program for drawing aesthetic RNA consensus diagrams with automated pair covariance recognition. Rfam uses this program both for drawing the human-annotated SS and the R-scape covariance-optimized structure. source [228] RNAcanvas A web app for drawing and exploring nucleic acid structures. webapp [229] RNAscape
Tools for general model building: C-alpha baton mode - trace the main chain of a protein by placing correctly spaced alpha-carbon atoms. Ca Zone -> Mainchain - convert an initial trace of the alpha-carbon atoms to a full main-chain trace. Place helix here - fit a sequence of amino acids in alpha helix conformation into density.
QC-Chain is a package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. QC3 a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
MNHN-Tree-Tools: MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien ...
Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems. An emerging trend is the blurring of boundaries between the visualization of 3D structures at atomic resolution, the visualization of larger complexes by cryo-electron microscopy , and the visualization of the location of ...
Nucleic acids consist of a chain of linked units called nucleotides. Each nucleotide consists of three subunits: a phosphate group and a sugar (ribose in the case of RNA, deoxyribose in DNA) make up the backbone of the nucleic acid strand, and attached to the sugar is one of a set of nucleobases.
The nucleotides on one strand base pairs with the nucleotide on the other strand. The secondary structure is responsible for the shape that the nucleic acid assumes. The bases in the DNA are classified as purines and pyrimidines. The purines are adenine and guanine. Purines consist of a double ring structure, a six-membered and a five-membered ...
Dia has special objects to help draw entity-relationship models, Unified Modeling Language (UML) diagrams, flowcharts, network diagrams, and simple electrical circuits. It is also possible to add support for new shapes by writing simple XML files, using a subset of Scalable Vector Graphics (SVG) to draw the shape.