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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
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.
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.
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 ...
Alignment Editor ― Within MEGA, the Alignment Editor is a tool that may be used for editing and building multiple sequence alignments. The Alignment Editor in MEGA includes an integrated tool for both ClustalW and MUSCLE programs. All actions take place in the Analysis Explorer, which can be found in the main menu of MEGA.
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 ...
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.