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Integrated Genome Browser: Java-based desktop genome browser: Linux, macOS, Windows: Common Public 1.0 GenoViz InterMine: Extensive data warehouse system for the analysis and integration of biological datasets written in Java and JavaScript Cross-platform: LGPL: University of Cambridge: LabKey Server
Fast detection of coding regions in short genome sequences: Dragon Promoter Finder Program to recognize vertebrate RNA polymerase II promoters: Vertebrates [7] EasyGene: 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 ...
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.
Integrated Genome Browser (IGB) (pronounced Ig-Bee) [1] is an open-source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.
Galaxy [2] is a scientific workflow, data integration, [3] [4] and data and analysis persistence and publishing platform that aims to make computational biology and other scientific disciplines accessible to research scientists that do not have computer programming or systems administration experience.
Indexes the genome with periodic seeds to quickly find alignments with full sensitivity up to four mismatches. It can map Illumina and SOLiD reads. Unlike most mapping programs, speed increases for longer read lengths. Yes Free, GPL [49] PRIMEX Indexes the genome with a k-mer lookup table with full sensitivity up to an adjustable number of ...
Strawberry A program for genome-guided transcripts reconstruction and quantification from paired-end RNA-seq. StringTie StringTie is an assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing ...
The first set of Perl codes of BioPerl was created by Tim Hubbard and Jong Bhak [citation needed] at MRC Centre Cambridge, where the first genome sequencing was carried out by Fred Sanger. MRC Centre was one of the hubs and birthplaces of modern bioinformatics as it had a large quantity of DNA sequences and 3D protein structures.