Results for "Genomic"
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FGENESH - Program for predicting multiple genes in genomic DNA sequences
FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et al. (2002) Science 296:79) and was used to produc...Tags: FGENESH, Program, predicting, multiple, genes, genomic, DNA, sequences
1955 days ago
UPhO: Scripts for homology and orthology assessment from genomic sequences.
UPhO finds orthologs with and without inparalogs from input gene family trees. Refer to the Documentation.pdf for more detailed explanations on its usage, installation and dependencies. Type UPhO.py -h for help. The only input requierement for UPhO is a tree (or trees) in Newick format in which ...Tags: UPhO, Scripts, homology, orthology, assessment, genomic, sequences
1930 days ago
Apollo: First instantaneous, collaborative genomic annotation editor available on the Web
Apollo is a plug-in for the JBrowse Genome Viewer. In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the ‘Information Editor’. ...Tags: Apollo, collaborative, genomic, annotation, editor, Web, genome
1793 days ago
RepeatModeler2: automated genomic discovery of transposable element families
RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/Repe...Tags: RepeatModeler2, automated, genomic, discovery, transposable, element, families
1608 days ago
- AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguish...
Tags: AccessSyRI, finding, genomic, rearrangements, sequence, differences, whole-genome, assemblies
1547 days ago
Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo: https://vgteam.github.io/sequenceTubeMap/Tags: Sequence, Tube, Maps, displays, multiple, genomic, sequences, tube, map, graphmap
1509 days ago
Phytozome v12.1: plant science community hub for accessing palnts genomic data
Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been seq...Tags: Phytozome, plant, science, community, hub, accessing, palnts, genomic, data, genome
1502 days ago
- gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.
Tags: gget, data, query, genomic, search
392 days ago
ReConPlot: an R package for the visualization and interpretation of genomic rearrangements
ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing customization of plots and the generation of publication-qua...Tags: ReConPlot, R, package, visualization, interpretation, genomic, rearrangements
135 days ago
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