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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 ...
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 ...
BLAT can be used to align DNA sequences as well as protein and translated nucleotide (mRNA or DNA) sequences. It is designed to work best on sequences with great similarity. The DNA search is most effective for primates and the protein search is effective for land vertebrates.
A tool to annotate phage genomes. Phages [43] SplicePredictor Method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models: Eukaryotes [44] VEIL Hidden Markov model to find genes in vertebrate DNA Server: Eukaryotes [45]
It takes a protein sequence and compares it to all possible translations of a DNA sequence. This is useful when looking for similar protein-coding regions in DNA sequences that haven't been fully annotated, like ESTs (short, single-read cDNA sequences) and HTGs (draft genome sequences).
At this step, sequencing reads whose quality have been improved are mapped to a reference genome using alignment tools like BWA [17] for short DNA sequence reads, minimap [18] for long read DNA sequences, and STAR [19] for RNA sequence reads. The purpose of mapping is to find the origin of any given read based on the reference sequence.
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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.