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Stothard Research Group

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

Servers

BASys - performs automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual and hyperlinked image output. BASys uses more than 30 programs to determine nearly 60 annotation subfields for each gene, including gene/protein name, GO function, COG function, possible paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, secondary structure, 3-D structure, reactions, and pathways. The textual annotations and images that are provided by BASys can be generated in approximately 24 hours for an average bacterial chromosome (5 megabases).
Availability: http://wishart.biology.ualberta.ca/basys/

BacMap - an interactive visual database containing all publicly available bacterial genomes. A fully labeled and zoomable genome map is provided for each genome. Sequence and text queries can be used to identify genes of interest, or maps can be navigated using a simple interface. BacMap is designed to serve as an intuitive and convenient tool for identifying orthologues and paralogues, studying operon conservation, and determining gene function.
Availability: http://bacmap.wishartlab.com/

CGView Server - a comparative genomics tool for circular genomes (plasmid, bacterial, mitochondrial, and chloroplast) that allows sequence feature information to be visualized in the context of sequence analysis results. A genome sequence is supplied to the program in FASTA, GenBank, EMBL, or raw format. Up to three comparison sequences (or sequence sets) in FASTA format can also be submitted. The CGView Server uses BLAST to compare the genome sequence to the comparison sequences, and then converts the results and any available feature information (from the GenBank, EMBL, or optional GFF file) or analysis information (from an optional GFF file) into a high-quality graphical map showing the entire genome sequence, or a zoomed view of a region of interest. Several options are available for specifying how the BLAST comparisons are conducted, and for controlling how results are displayed.
Availability: http://stothard.afns.ualberta.ca/cgview_server/

DrugBank - a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information.
Availability: http://www.drugbank.ca/

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.
Availability: https://www.gview.ca/

HMDB - a freely available electronic 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.
Availability: http://www.hmdb.ca/

PolySearch - supports more than 50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is "Given X, find all Y's" where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences.
Availability: http://wishart.biology.ualberta.ca/polysearch/

PROSESS - a web server designed to evaluate and validate protein structures solved by either X-ray crystallography or NMR spectroscopy. PROSESS integrates a variety of previously developed, well-known and thoroughly tested methods.
Availability: http://www.prosess.ca/

Sequence Extractor - generates a clickable restriction map and PCR primer map of a DNA sequence. Protein translations and intron/exon boundaries are also shown. Use Sequence Extractor to build DNA constructs in silico.
Availability: http://bioinformatics.org/seqext/

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.
Availability: http://bioinformatics.org/sms2/

Downloads

CGView - a Java package for generating high quality, zoomable 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, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics 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.
Developed by: Paul Stothard.
Availability: http://bioinformatics.org/cgview/

CGView Comparison Tool (CCT) - a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. 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 the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation.
Developed by: Paul Stothard and Jason Grant.
Availability: http://stothard.afns.ualberta.ca/downloads/CCT/

NGS-SNP - this collection of scripts annotates raw SNP lists returned from programs such as Maq. SNPs are classified as synonymous, nonsynonymous, 3' UTR, etc. regardless of whether or not they match existing SNP records. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate whether or not the SNP-altered residue exhibits co-evolution with other residues in the protein, the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A "Model_Annotations" field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species.
Developed by: Paul Stothard, Jason Grant, and Xiaoping Liao.
Availability: http://stothard.afns.ualberta.ca/downloads/NGS-SNP/.