Results for "analysis"
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GIGGLE: a search engine for large-scale integrated genome analysis
GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existi...Tags: GIGGLE, search, engine, large-scale, integrated, genome, analysis
2316 days ago
PGAP-X: Extension on pan-genome analysis pipeline
PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different conservative levels, and genetic variation from pa...Tags: PGAP-X, Extension, pan-genome, analysis, pipeline
2303 days ago
MGcV: the microbial genomic context viewer for comparative genome analysis
MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV: Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by selecting the type of identifier and pasting identifiers (one per line) or b...Tags: MGcV, microbial, genomic, context, viewer, comparative, genome, analysis
2297 days ago
GenomeTools: The versatile open source genome analysis software
The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules. If ...Tags: GenomeTools, versatile, open, source, genome, analysis, software
2288 days ago
Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analys...Tags: Mesquite, modular, system, evolutionary, analysis
2254 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs ...Tags: bpRNA, large-scale, automated, annotation, analysis, RNA, secondary, structure
2183 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in output for easy plotting. gcp: K-mer GC Pr...Tags: KAT, K-mer, analysis, toolkit, quality, control, NGS, datasets, genome, assemblies
1991 days ago
EGAD: Ultra-fast functional analysis of gene networks
With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficient tools to calculate functional properties in networks based on the guilt-by-association principle. These allow rapid controlled comparisons and analyses. Two of the core features...Tags: EGAD, Ultra-fast, functional, analysis, gene, networks
1978 days ago
