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Essential Resources
- BioBIKE portal
- Different routes to CyanoBIKE instances:
usual,
alternate,
- Alternate routes to ViroBIKE instances:
usual,
alternate,
- Only route to PhAnToMe BioBIKE instance (at the moment):
usual
- BioBIKE meeting rooms - Use it to meet others in the class or in the project
Click "Presenter Login" if you have a password
Click "Participant Login" if you don't
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
- 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
- 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.
- VCU Library
Apart from its many other merits, the library enables you to reach electronic journal articles that would otherwise be restricted.
Research Opportunities (Summer 2013 and perhaps beyond)
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