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The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes [8] [9] EuGene: Integrative gene finding: Prokaryotes, Eukaryotes [10] [11] FGENESH: HMM-based gene structure prediction: multiple genes, both chains: Eukaryotes [12] FrameD: Find genes and frameshift in G+C rich prokaryote ...
Agilent Technologies RFLP Decoder Software, Fish Species; Applied Biosystems GeneMapper; Joint BioEnergy Institute j5; CLC bio CLC DNA Workbench Software; CLC bio CLC Free Workbench Software; CLC bio CLC Sequence Viewer; CLC bio Protein Workbench Software; DNASTAR Lasergene; Geneious; LabVantage Solutions Inc. LabVantage Sapphire; LabVantage ...
GeneMark is a generic name for a family of ab initio gene prediction algorithms and software programs developed at the Georgia Institute of Technology in Atlanta.Developed in 1993, original GeneMark was used in 1995 as a primary gene prediction tool for annotation of the first completely sequenced bacterial genome of Haemophilus influenzae, and in 1996 for the first archaeal genome of ...
Varies depending on tool Collaborative project GenGIS: Application that allows combining digital map data with information about biological sequences collected from the environment Windows, macOS: GPL: Collaborative project GenoCAD: A computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar ...
Salmon is a software tool for computing transcript abundance from RNA-seq data using either an alignment-free (based directly on the raw reads) or an alignment-based (based on pre-computed alignments) approach. It uses an online stochastic optimization approach to maximize the likelihood of the transcript abundances under the observed data.
Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.
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UGENE integrates dozens of well-known biological tools, algorithms, and original tools in the context of genomics, evolutionary biology, virology, and other branches of life science. UGENE provides a graphical user interface (GUI) for the pre-built tools so biologists with no computer programming skills can access those tools more easily.