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Free, GPL2 ALLALIGN For DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater, MSA or within a single molecule. Similar alignments are grouped together for analysis. Automatic repetitive sequence filter. Both Local E. Wachtel 2017 Free AMAP: Sequence annealing: Both: Global: A. Schwartz and L. Pachter: 2006: BAli-Phy
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
The source code for the package is distributed freely and compiled binaries are available for Linux, macOS and Windows platforms. As of 2017, the Genome Biology paper describing the original Bowtie method has been cited more than 11,000 times. [3] Bowtie is open-source software and is currently maintained by Johns Hopkins University.
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
PHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools Cross-platform: GPL v2 Open Bioinformatics Foundation: Biopython: Python language toolkit Cross-platform: Biopython [2] Open Bioinformatics Foundation: BioRuby: Ruby language toolkit Linux, macOS, Windows [3] GPL ...
Generates models for unusual DNA, RNA: Free, GPL: New Jersey University: NAnoscale Molecular Dynamics ... List of protein structure prediction software;
FASTA is pronounced "fast A", and stands for "FAST-All", because it works with any alphabet, an extension of the original "FAST-P" (protein) and "FAST-N" (nucleotide) alignment tools. Mappers timeline (since 2001). DNA mappers are plotted in blue, RNA mappers in red, miRNA mappers in green and bisulphite mappers in purple.
The profile-HMM implementation used in the HMMER software was based on the work of Krogh and colleagues. [3] HMMER is a console utility ported to every major operating system, including different versions of Linux, Windows, and macOS. HMMER is the core utility that protein family databases such as Pfam and InterPro are based upon.