Results for "identification"
Tags
DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate tha...Tags: DAVI, deep, alignment, variant, identification, tool, snp
1130 days ago
- RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly. Availability: RAMI is licensed under GNU GPL and can be run or downloaded from&n...
Tags: RAMI, tool, identification, characterization, phylogenetic, clusters, microbial, communities
2447 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to achieve very high accuracy on short reads. Unlike o...Tags: Rapid, identification, high-confidence, taxonomic, assignments, metagenomic, data, RITA
2335 days ago
- TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, repres...
Tags: TAREAN, Computational, tool, identification, characterization, satellite, DNA, unassembled, short, reads
2166 days ago
DMINDA2: an integrated web server for DNA motif identification and analyses
DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses More at http://bmbl.sdstate.edu/DMINDA2/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086085/Tags: DMINDA2, integrated, web, server, DNA, motif, identification, analyses
1538 days ago
PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends on performing a all-vs-all sequence comparison,...Tags: PyParanoid, pipeline, rapid, identification, homologous, gene, families, set, genomes
1345 days ago
IgBLAST 1.17 is now available with improved identification of productive V gene sequences
A new release of IgBLAST (1.17), the popular package for classifying and analyzing immunoglobulin and T cell receptor sequences, is now available on the web and from the FTP site. The updated package is better at identifying productive V gene sequences. We added a new fie...Tags: IgBLAST, improved, identification, productive, V gene, sequences
1265 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the ne...Tags: PaReBrick, Parallel, Rearrangements, Breaks, identification, toolkit
924 days ago
- fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect viral infectious diseases, like COVID-19. This to...
Tags: virus, detect, fast, identification
860 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
35 days ago
