BNFO 301 
Introduction to Bioinformatics
Resources and Links
Spring 2015 

Essential resources
Other useful resources
Summer undergraduate research opportunities


Essential Resources

Other Useful Resources

  • Abbreviations
    List of nucleotide, amino acid abbreviations, and genetic code
  • Bioinformatics resources on web
    Annotated list of web-based programs for analyzing DNA and protein sequences
  • Chi-squared calculator (courtesy of John Walker, Fourmilab)
    Chi-square test probability calculator
  • Chi-squared table (courtesy of Alexei Sharov, Virginia Tech)
    Interpret Chi-square values for a given level of significance
  • Codon usage tables (courtesy of Yasukazu Nakamura)
    Codon frequencies for large number of sequenced genomes
  • DNA dot plots (courtesy of Colorado State U.)
    Compares two nucleic acid sequences
  • GeneMark
    Predict open reading frames in DNA sequences
  • Genetic code
    Useful on line reference to recall code, types of amino acids, and their abbreviations
  • ICTVdB
    International Committee on the Taxonomy of Viruses Database: Descriptions of taxa, pictures
  • Molecular Biology of the Cell (Bruce Alberts et al, 2002; 4th edition)
    Molecular Cell Biology text book. Free for searching but not browsing.
  • Mycobacteriophage DataBase
    A site summarizing what is known concerning mycobacteriophages, particularly new phages analyzed by classes such as ours
  • NCBI
    National Center for Biotechnology Information: Home of Blast, Entrez, much else
  • PhAnToMe
    A loose group of those dedicated to the analysis of phage genomes. Not to be confused with the PhAnToMe BioBIKE instance
  • Protein Data Base
    Large collection of data concerning protein structure and sequence
  • Protein Explorer and help
    Site to display molecular structures, offering more power than FirstGlance, at the cost of a more complicated interface
  • Proteopedia
    Repository of protein structures and educational tools
  • Sequence analysis tools (courtesy of CBS, Technical University of Denmark)
    Collection of online DNA and protein analysis tools
  • Sequence Logos (courtesy of Steven Brenner, U. California, Berkeley)
    Graphical representation of nucleotide or amino acid frequencies in aligned sequences
  • t-test calculator (courtesy of GraphPad)
    You provide either raw data or (mean, standard deviation, number of samples), it returns the t-test score and the probability of score arising if both samples were taken from the same population.
  • t-test probability calculator (courtesy of Daniel Soper)
    You provide score from t-test and degrees of freedom, it returns probability of score arising if both samples were taken from the same population.
  • Taxonomy Browser (courtesy of National Center for Biotechnology Information)
    Enter the name of an organism and find out its classification. You can click on higher order taxons (e.g. families) to find other related organisms.
  • VCU Library
    Apart from its many other merits, the library enables you to reach electronic journal articles that would otherwise be restricted.

Summer Undergraduate Research Opportunities (deadlines in parentheses)

VCU opportunities

Outside opportunities for undergraduate summer internships