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DNA origami object from viral DNA visualized by electron tomography. [1] The map is at the top and atomic model of the DNA colored below. (Deposited in EMDB EMD-2210) . DNA origami is the nanoscale folding of DNA to create arbitrary two- and three-dimensional shapes at the nanoscale.
Algorithm and program for comparing primary biological sequence information, including DNA and protein sequences. Cross-platform: Public domain: National Center for Biotechnology Information: CP2K: Perform atomistic simulations of solid state, liquid, molecular and biological systems, written in Fortran 2003. Linux, macOS, Windows: GPL and LGPL
A program for predicting unique local RNA structures in large sequences with unusually stable folding. 1: None: Yes: sourcecode webserver [153] Xrate: a program for analysis of multiple sequence alignments using phylogenetic grammars, that may be viewed as a flexible generalization of the "Evofold" program. any: Yes: Yes: sourcecode [97] Notes
This page is a subsection of the list of sequence alignment software. Multiple alignment visualization tools typically serve four purposes: Aid general understanding of large-scale DNA or protein alignments; Visualize alignments for figures and publication; Manually edit and curate automatically generated alignments; Analysis in depth
Nucleic acid design can be used to create nucleic acid complexes with complicated secondary structures such as this four-arm junction. These four strands associate into this structure because it maximizes the number of correct base pairs, with A's matched to T's and C's matched to G's.
Basically, Sankoff algorithm is a merger of sequence alignment and Nussinov [7] (maximal-pairing) folding dynamic programming method. [22] Sankoff algorithm itself is a theoretical exercise because it requires extreme computational resources (O (n3m) in time, and O (n2m) in space, where n is the sequence length and m is the number of sequences).
Multiple Expectation maximizations for Motif Elicitation (MEME) is a tool for discovering motifs in a group of related DNA or protein sequences. [1] MEME takes as input a group of DNA or protein sequences and outputs as many motifs as requested up to a user-specified statistical confidence threshold. MEME uses statistical modeling techniques to ...
A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G , C , A and T . This is then reported as a text string, called a read.