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EzTaxon-e: database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences; NCBI Taxonomy: a taxonomic database operated by NCBI and concentrating on all taxa for which DNA sequences are available (those sequences are stored by GenBank, another database operated by NCBI).
Human, Mus musculus, Arabidopsis thaliana, Drosophila melanogaster [32] [33] mGene Support-vector machine (SVM) based system to find genes: Eukaryotes [34] mGene.ngs SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays: Eukaryotes [35] MORGAN: Decision tree system to find genes in vertebrate DNA: Eukaryotes [36 ...
The Arabidopsis genome and annotations can be visualized using the interactive SeqViewer and GBrowse tools. TAIR’s biocurators are responsible for acquiring and integrating data from the research literature (functional annotation) [ 2 ] as well as for assisting the community in using Arabidopsis data and tools.
A computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar rules. Linux, macOS, Windows: Apache License 2.0 GenoCAD Team (Virginia Bioinformatics Institute) Genomespace: Centralized web application that provides data format transformations and facilitates connections with other bioinformatics ...
Primer Premier is a bioinformatics software used for various PCR applications. It supports the design of degenerate primers for amplifying a related set of nucleotide sequences for the detection of common traits amongst organisms, as well as to determine heredity. [1] The software also designs tagged and nested primers for multiplex PCR ...
These tools are used to optimize the design of primers for target DNA or cDNA sequences. Primer optimization has two goals: efficiency and selectivity. Efficiency involves taking into account such factors as GC-content, efficiency of binding, complementarity, secondary structure , and annealing and melting point (Tm) .
Gene Designer is a computer software package for bioinformatics. [1] [2] It is used by molecular biologists from academia, government, and the pharmaceutical, chemical, agricultural, and biotechnology industries to design, [3] clone, and validate genetic sequences. It is proprietary software, released as freeware needing registration.
OLIGO Primer Analysis Software is a software for DNA primer design. [ 1 ] [ 2 ] The first paper describing this software was published in 1989. [ 3 ] The program is a real time PCR primer and probe search and analysis tool.