Stothard Research Group


The 1000 Bulls Project paper on genes regulating body size has been published in Nature Genetics


Proksee Server (beta) - an updated version of the popular CGView Server for the analysis and visualization of bacterial genomes. This version includes integrated genome annotation tools and a new CGView engine written in JavaScript that allows for rapid zooming to the DNA sequence level. Extensive options are available for customizing maps and highlighting features of interest.

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.
site: https://paulstothard.github.io/sequence_manipulation_suite/
code: https://github.com/paulstothard/sequence_manipulation_suite


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 databases.
docs: https://paulstothard.github.io/cgview/
code: https://github.com/paulstothard/cgview

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 customized.
docs: https://paulstothard.github.io/cgview_comparison_tool/
code: https://github.com/paulstothard/cgview_comparison_tool

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.