Results for "analysis"
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JSON (JavaScript Object Notation) is a lightweight data-interchange format. It is easy for humans to read and write. It is easy for machines to parse and generate. It is based on a subset of the JavaScript Programming Language, Standard ECMA-262 3rd Edition - December 1999. JSON is...Tags: Bioinformatics, Analysis, Format, JSON
2582 days ago
- UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and i...
Tags: Bioinformatics, Analysis, Plot, UpSetR, Shiny, App, R
2572 days ago
- DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies Our work is published in Scientific Reports: Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologi...
Tags: Bioinformatics, Analysis, Assembly, Genome, PacBio, Long, DBG2OLC
2567 days ago
Enrichr: a comprehensive gene set enrichment analysis
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and down...Tags: Bioinformatics, Analysis, Enrichment, Enrichr, Web, Server, GO, Pathway, Genes, BED, Ontologies, Drug, Cell, Disease
2559 days ago
- A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides in bacterial genomes contain useful, albeit weak, phylogenetic signals. Even though tetra-nucleotide analysis (TNA) utilizes the informat...
Tags: Bioinformatics, Tetra-Nucleotide, Analysis, Frequency, DNA, Phylogeny, Algorithms
2552 days ago
CLA: Contig-Layout-Authenticator
To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CL...Tags: Bioinformatics, Analysis, Scaffolding, CLA, Contig
2551 days ago
- This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high quality assemblies of bacterial sequence data. The bacterial sample used in this tutorial will be referred to simply as “Species” s...
Tags: Bioinformatics, Analysis, Assembly, Genome, Annotation, Prokaryotes, Bacteria
2551 days ago
- A new “Download assemblies” button is now available in the Assembly database. This makes it easy to download data for multiple genomes without having to write scripts. For example, you can run a search in Assembly and use check boxes (see left side of screenshot below) to r...
Tags: Bioinformatics, Analysis, Assembly, Genome, Annotation, NCBI, Download
2541 days ago
NCBI Prokaryotic Genome Annotation Pipeline
NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, sma...Tags: Bioinformatics, Analysis, Assembly, Genome, Annotation, NCBI, Pipeline, Prokaryotes
2540 days ago
Synteny Portal: a web-based application portal for synteny block analysis
Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and downlo...Tags: Synteny, Portal, Web-based, Application, Synteny, Block, Analysis
2532 days ago
