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Combines DNA and Protein alignment, by back translating the protein alignment to DNA. DNA/Protein (special) Local or global: Wernersson and Pedersen: 2003 (newest version 2005) SAGA Sequence alignment by genetic algorithm: Protein: Local or global: C. Notredame et al. 1996 (new version 1998) SAM Hidden Markov model: Protein: Local or global: A ...
The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
For normal Protein-DNA alignment tools, they first choose one of three frames to translate the DNA into a protein sequence, and then compare it with the given protein. Such alignment is based on the assumption that the DNA translation frame is not interrupted for the whole DNA strand. However, this is not generally true.
EMBOSS is a free c software analysis package developed for the needs of the molecular biology and bioinformatics user community. [1] The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.
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 ...
Wise2 - aligns a protein against a DNA sequence allowing frameshifts and introns; FastY - compare a DNA sequence to a protein sequence database, allowing gaps and frameshifts; Path Archived 2011-07-19 at the Wayback Machine - tool that compares two frameshift proteins (back-translation principle)
Ideal DNA/RNA - build an ideal DNA or RNA fragment. Find ligands - find and fit a model to any small molecule which may be bound to the macromolecule. Tools for moving existing atoms: Real space refine zone - optimize the fit of the model to the electron density, while preserving stereochemistry. Regularize zone - optimize stereochemistry.
Graphical analysis tool to find all open reading frames: Prokaryotes, Eukaryotes [40] Regulatory Sequence Analysis Tools: Series of modular computer programs to detect regulatory signals in non-coding sequences: Fungi, Prokaryotes, Metazoa, Protist, Plants [41] [42] PHANOTATE: A tool to annotate phage genomes. Phages [43] SplicePredictor