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Software for ultra fast local DNA sequence motif search and pairwise alignment for NGS data (FASTA, FASTQ). DNA: Hepperle D (www.sequentix.de) 2020 Genoogle Genoogle uses indexing and parallel processing techniques for searching DNA and Proteins sequences. It is developed in Java and open source. Both: Albrecht F: 2015 HMMER
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
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.
MAFFT is widely considered to be one of the most accurate and versatile tools for multiple sequence alignment in bioinformatics. In fact, studies have shown that MAFFT performs exceptionally well when compared to other popular algorithms such as ClustalW and T-Coffee, particularly for larger datasets and sequences with high degrees of ...
Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics. [3] 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 ...
This tool is useful when the reading frame of the DNA sequence is uncertain or contains errors that might cause mistakes in protein-coding. BLASTx provides combined statistics for hits across all frames, making it helpful for the initial analysis of new DNA sequences. [16] BLASTp Protein sequence being compared against nr database using BLASTp.
The higher the score of the shuffled sequences the less significant the matches found between original database and query sequence. [5] The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.
DNADynamo is a general purpose DNA and Protein sequence analysis package that can carry out most of the functions required by a standard research molecular biology laboratory DNA and Protein Sequence viewing, editing and annotating; Contig assembly and chromatogram editing including comparison to a reference sequence to identify mutations
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