Proksee Server (beta) - an updated
version of the popular CGView Server for the analysis and
visualization of bacterial genomes. This version includes integrated
that allows for rapid zooming to the DNA sequence level. Extensive
options are available for customizing maps and highlighting features
DrugBank - a unique bioinformatics and
cheminformatics resource that combines detailed drug data with
comprehensive drug target information.
GView - a java package used to display
and navigate bacterial genomes. GView is useful for producing
high-quality genome maps for use in publications and websites, or as a
visualization tool in a sequence annotation pipeline. Users can
interact with the genome using a powerful pan-and-zoom interface, or
GView can write static images of a genome to a file. GView can draw a
genome using either circular or linear layouts, with additional layout
types planned for future release.
HMDB - a database containing detailed
information about small molecule metabolites found in the human body.
It is intended to be used for applications in metabolomics, clinical
chemistry, biomarker discovery and general education.
The Sequence Manipulation Suite - a
collection of simple programs for generating, formatting, and
analyzing short DNA and protein sequences. The Sequence Manipulation
Suite is commonly used by molecular biologists, for teaching purposes,
and for program and algorithm testing.
CGView - a Java package for generating
high quality, navigable maps of circular genomes. Its primary purpose
is to serve as a component of sequence annotation pipelines. Feature
information and rendering options are supplied to the program using an
XML file or a tab-delimited file. CGView converts the input into a
graphical map (PNG, JPG, or SVG format), complete with labels, a
title, and legends. In addition to the default full view map, the
program can generate a series of hyperlinked maps showing expanded
views. The linked maps can be explored using any web browser, allowing
rapid genome browsing, and facilitating data sharing. The feature
labels in maps can be hyperlinked to external resources, allowing
CGView maps to be integrated with existing web site content or
CGView Comparison Tool (CCT) - The
CGView Comparison Tool (CCT) is a package for visually comparing
bacterial, plasmid, chloroplast, and mitochondrial sequences. The
comparisons are conducted using BLAST, and the BLAST results are
presented in the form of graphical maps that can also show sequence
features, gene and protein names, COG category assignments, and
sequence composition characteristics. CCT can generate maps in a
variety of sizes, including 400 Megapixel maps suitable for posters.
Comparisons can be conducted within a particular species or genus, or
all available genomes can be used. The entire map creation process,
from downloading sequences to redrawing zoomed maps, can be completed
easily using scripts included with CCT. User-defined features or
analysis results can be included on maps, and maps can be extensively
ncbi_search - a Perl script that uses
NCBI's Entrez Programming Utilities to perform searches of NCBI
databases. The script can be used to search any of the available
databases using the Entrez query syntax, and records can be returned
in a variety of formats.
genotype_conversion_file_builder - a
pipeline for determining the genomic location and transformation rules
for the variants described in Illumina or Affymetrix genotype panel
manifest files. The pipeline uses the Nextflow workflow management
system, which makes it easy to deploy on clusters and in the cloud.