Canadian Bioinformatics Help Desk -- CBHD Servers

Web Servers

Please note: If you have one or more web servers that you would like to add to our servers page, or know of any bioinformatics servers that we should mirror from our web servers page, please send an email to Help Desk (info@gchelpdesk.ualberta.ca).
	PROTEUS	Proteus is a high-performing integrated web server and a stand-alone application that employs three high-performing de novo structure prediction methods (PSIPRED, JNET and TRANSSEC, a locally developed predictor), a jury-of-experts consensus tool and a robust PDB-based structure alignment process to generate all of its secondary structure predictions.

	PREDITOR	PREDITOR is a program for PREDIcting phi, psi, omega and chi-1 TORsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology. PREDITOR 30°-accuracy of predicting phi and psi is close to 90%. The average chi-1 accuracy is 84% while the omega accuracy is 99.98% for trans peptide bond identification and 93% for cis peptide bond identification. Overall, the program is 35X faster and its predictions are approximately 20% better than existing methods.

	DrugBank	The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

	BASys	BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences.

	MovieMaker	MovieMaker is a web server that generates short, downloadable movies of protein dynamics. It accepts PDB files or PDB accession numbers as input and automatically outputs colorful animations covering a wide range of protein motions and other dynamic processes.

	BacMap	BacMap is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.

	CGView	CGView is a Java package for generating high quality, zoomable maps of circular genomes.

	PlasMapper	The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input.

	SuperPose	SuperPose is a protein superposition server. From a superposition of two or more structures, SuperPose generates sequence alignments, structure alignments, PDB coordinates, RMSD statistics, difference distance plots, and interactive images of the superimposed structures.

	CyberCell Database	A comprehensive E. coli specific database, containing genomic, proteomic and metabolomic information.

	GelScape	A web-based gel viewing and annotation system.

	VADAR	VADAR (Volume, Area, Dihedral Angle Reporter)—this web server quantitively evaluates protein structures using their PDB coordinates.

	SHIFTX	A web server that predicts ¹H, ¹³C, and ¹⁵N protein chemical shifts using the 3D structure (PDB coordinates) of the protein of interest.

	SHIFTY	A web server for predicting protein chemical shifts using only amino acid sequence information.

	SHIFTZ	A web server that calculates ¹H, ¹³C, and ¹⁵N backbone chemical shifts of peptides and proteins using only their sequence and backbone dihedral angles as input.

	SimPred	A web server that predicts ¹H, ¹³C, and ¹⁵N backbone chemical shifts of peptides and proteins using only the amino acid sequence and the predicted (known) secondary structure as input.

	SHIFTCOR	A web server that compares, corrects and references chemical shift assignments using 3D structure (PDB coordinates) of assigned proteins.
	SHIFTOR	A web server that predicts protein backbone dihedral angles (phi and psi) from observed ¹H, ¹³C, and ¹⁵N chemical shifts.

	SASS	A web server that allows you to obtain sequential assignments and a 3D structure for your favorite protein using only its sequence and at least one (HNCACB) peak list as input.

	DynaMR	A web server predicts backbone mobilities (order parameters) from observed chemical shifts.

	Thrifty	A web server that rapidly generates 3D protein structures (PDB coordinates) from their corresponding chemical shift assignments.

	HOMODELLER	A web server that rapidly generates 3D protein structures (PDB coordinates) from their corresponding protein sequence.

	RefDB	The Re-referenced Protein Chemical Shift Database (RefDB) is a database of carefully corrected and re-referenced chemical shifts, derived from the BioMagResBank.

	PepMake	A web server that generates a PDB coordinate file for a polypeptide using only the sequence and backbone dihedral angles as input.

	diNucleotide Tandem Repeat Finder	Searches a FASTA DNA file line-by-line for the presence of di-nucleotide tandem repeats.

	Osprey	Osprey calculates optimal oligonucleotides for a range of tasks: sequence assembly (both contig walking and polishing, with Staden assembly augmented functionality), differential expression, and microarrays (cDNA and spotted oligos).

	Hydrophobicity Profiler	This web server reads a FASTA-formatted protein sequence, calculates its hydrophobicity profile according to the user-selected window size and hydrophobicity scale, and a returns a graphical image of the profile.

	REquest	This web server reads a FASTA-formatted DNA sequence, searches for all restriction endonuclease sites (from the enzyme set selected by the user), and a returns a list of all enzymes, their cleavage sites, and the fragments produced.

	OligoFinder	This web server searches for optimal oligonucleotides for spotted arrays. It reads a FASTA-formatted DNA sequence, searches for primer sequences that fall within the user-designated melting temperature range, and carries out a BLAST check to ensure that there is no more than one high quality match.

	SEQUEROME	SEQUEROME is an i-Propaedia OR a 'Sequence profiling tool' to get the maximum out a 'sequence alignment report', e.g. BLAST, without having to leave the browser session. Some of the advantages include: 1) 'Gene-sequence to Probable structure/function' Interface in a single browser session, 2) Performing parallel searches and Sequence manipulation/analysis (using popular bioinformatics tools), 3) 'One-Box Any-sequence' entry format, and 4) Generation of a panel of icons recording the Search history for instant retrieval.

	InstaSeq	InstaSeq is a Google-powered search tool that provides instant access to all related records and information on the World Wide Web about an input fragment of DNA, RNA or protein sequence. There is also full access to SEQUEROME, for more detailed analysis.

	FlexArray	FlexArray is a Microsoft Windows software package for statistical analysis of microarray data. FlexArray combines the ease-of-use with a comprehensive set of statistical utilities. It offers a wide variety of useful visualization options, a rich interactive environment, full analysis history, a plug-in interface for algorithms and plots, analysis protocol support, and more. FlexArray currently supports Affymetrix expression GeneChip© microarrays, and Illumina expression BeadChip© arrays. FlexArray is free to academic researchers, and it was created with funding from Genome Quebec.

Automated Splice Site Analysis	ASSA	This web interface provides a tool to predict the effects of sequence changes that alter mRNA splicing in human diseases.

The Canadian Bioinformatics Help Desk, as part of the Integrated and Distributed Bioinformatics Platform for Genome Canada, is supported by Genome Alberta, in partnership with Genome Canada and other co-funding partners. Genome Canada is a not for profit corporation that is leading Canada's national strategy on genomics with $600 million in funding from the federal government.

This site is maintained by Canadian Bioinformatics Help Desk and was last updated on January 19 2010 14:35:06.
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