Tools

In silico Tools

  • Alignment Visualization Tool, ESPrit: A Visualization tool for protein alignments. 3D structure is required
  • Bepipred: linear epitope prediction available at the IEDB analysis resource webpage for b cells antibody epitope prediction
  • Easyfig: Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI)
  • FASTA Unique Sequence: Transform FAST files into a single file by eliminating the spaces
  • Genomics tools: Multipurpose genomic toolbox
  • Jmol: in silico tool used for molecular modelling chemical structures in 3-dimensions. This tool has to be downloaded
  • Mauve: Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion
  • MultiQC: MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools
  • Phage Annotation(PHASTER): Annotation tool for bacteriophage genomes
  • Prediction of transmembrane helices
  • Promoter analysis (virtual footprints): Determine regulons and binding boxes
  • Promoter prediction: Predict eukaryotic and bacteria promoter regions
  • Protter: interactive protein feature visualization. It is useful in visualizing the sequence, topology and annotations of individual proteins
  • Protein Analysis tools: Multipurpose protein analysis toolbox
  • PSORTb: Subcellular localization of bacterial proteins.
  • Rapid Annotation (RAST): Annotation tool for bacterial genomes. Could be utilized for bacteriophages but is not recommended.
  • Reffinder: Tool to determine the best reference gene for qPCR assays
  • Signal sequence peptide detection
  • Vaxign: vaccine target prediction and analysis system based on the principle of reverse vaccinology. It is used to predict subcellular localization, adhesin probability and trans-membrane helices necessary in the characterization of proteins that can be used as potential vaccine candidates
    • Vaxitop internally developed program in the Vaxign database that can be used to predict T cell epitopes binding to MHC I and II based on the reverse vaccinology approach
  • Venny 2.1.0: An interactive tool for comparing lists with Venn's diagrams
  • ViralZone-Continuing Education: Viruses topics

Contact

Ocean Sciences

230 Elizabeth Ave, St. John's, NL, CANADA, A1B 3X9

Postal Address: P.O. Box 4200, St. John's, NL, CANADA, A1C 5S7

Tel: (709) 864-8000