Results for "genes"
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ncbi-datasets-cli -- Quickstart: command line tools !
Install and use the NCBI Datasets command line tools The NCBI Datasets datasets command line tools are datasets and dataformat . Use datasets to download biological sequence data across all domains of life from NCBI. Use dataformat to convert metadata fr...Tags: ncbi-datasets-cli, database, download, ncbi, genome, genes, datasets
878 days ago
GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes
A phylogeny based comparative genomics software to analyze the genetic environment of genes. The user can select one or several taxa and provide one or several reference protein(s). Genomes and plasmids (based on user choice) will be downloaded from the NCBI Assembly/NR database and searched for ...Tags: GEnView, phylogeny, comparative, genomics, software, analyze, genetic, environment, genes
857 days ago
Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes. Our goal was to make it straightforward to work from a combination of input sources including annotated contigs in Genbank format and FASTA files containing CDSs. It uses several state of the art ...Tags: Orthoflow, workflow, phylogenetic, inference, genome-scale, datasets, protein-coding, genes
71 days ago
doubletrouble: identify duplicated genes from whole-genome protein sequences and classify
doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v....Tags: doubletrouble, identify, duplicated, genes, whole-genome, protein, sequences, classify
59 days ago
bacLIFE: an automated genome mining tool for identification of lifestyle associated genes
bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and biosynthetic gene clusters associated with each l...Tags: bacLIFE, automated, genome, mining, tool, identification, lifestyle, associated, genes
49 days ago
RCircos: an R package for Circos 2D track plots
RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate comple...Tags: Bioinformatics, NGS, R, Rcircos, Package, Plot, Circle, Genome, Genes, Visualization
2904 days ago
- A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function. http://biogps.org/#goto=welcome
Tags: Bioinformatics, BioGPS, Genes, Prediction, Function
2902 days ago
- statistical analysis and visulization of functional profiles for genes and gene clustersBioconductor version: Release (3.3)This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.Author: Guangchuang Yu <guangchuangyu at gmail.com>...
Tags: Bioinformatics, clusterProfiler, GO, R, Package, Omics, Genes, Cluster
2877 days ago
- DarkHorse is a bioinformatic method for rapid, automated identification and ranking of phylogenetically atypical proteins on a genome-wide basis. It works by selecting potential ortholog matches from a reference database of amino acid sequences, then using these matches to calculate a lineag...
Tags: Bioinformatics, HGT, Genes, Horizontal, Transfer, Method, Tools, DarkHorse
2872 days ago
- Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervis...
Tags: Bioinformatics, Analysis, NGS, Braker, Annotation, Genes, Predictions, Genome
1948 days ago
