Help Desk/Tools for Proteomics - Genome Canada Bioinformatics Innovation Centre

Software Tools and Databases:
The Help Desk offers many software tools and databases to the research community. For a complete list and links visit http://gchelpdesk.ualberta.ca/servers. Some important Help Desks web servers and tools are as follows:

PPT-DB (Protein Property Prediction and Testing Database is a database of databases. It houses more than 20 carefully curated databases, each of which contain commonly predicted protein property information.
CS23D (Chemical Shift to 3D Structure) is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input. Unlike conventional NMR methods which require NOE and/or J-coupling data, CS23D uses only chemical shift information to generate a 3D structure of the protein of interest. CS23D accepts chemical shift files in either SHIFTY or BMRB formats and produces a set of PDB coordinates for the protein in about 10-15 minutes.
BioSpider is a robust tool designed to scan the web for chemical and/or biological information. BioSpider brings together data from a large variety of databases, uses its own set of predictive programs, and integrates chemical (metabolite, ligand, cofactor and drug) data into its biological (sequence, function, pathway, etc.) reporting.
PolySearch is a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs, and metabolites. PolySearch supports more than 50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases.
BASys (Bacterial Annotation System) 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 provided by BASys can be generated in approximately 24 hours for an average bacterial chromosome (5 Megabases).
PlasMapper automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid sequences up to 20,000 bp may be annotated and displayed. Plasmid figures may be rendered in PNG, JPG, SVG, or SVGZ format. PlasMapper supports an extensive array of display options.
BacMap is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes. In these maps, gene labels are hyperlinked to detailed textual annotations. Maps can be explored manually or with the help of BacMap's built in text search and BLAST search. In BacMap, several charts illustrating the proteomic and genomic characteristics of each chromosome are available. Flat file versions of the BacMap gene annotations, gene sequences, and protein sequences can be downloaded.
CGView is 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, as a means of generating visual output suitable for the web. 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, legends, and footnotes. 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. For examples of the various output types, see the CGView gallery.

The Help Desk encourages registration for its services. Registering for the Help Desk benefits everyone by:

Sharing contact information with other Canadian researchers in the directory of Canadian bioinformaticians.
Receiving important updates about Help Desk news, events, conferences, and training sessions.
Receiving update notices for preferred bioinformatics software.
Submitting software into the bioinformatics software repository.
Submitting useful bioinformatics links into the bioinformatics links repository (future attraction).

To register now, visit http://gchelpdesk.ualberta.ca/user/register.php