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Entropy

Shannon Entropy-Two

  Entropy-Two   Entropy-One   Entropy Readme   Entropy Options  

Purpose: These tools apply Shannon Entropy as a measure of variation in DNA and protein sequence alignments. ENTROPY-TWO compares two sets of aligned sequences (named query and background sequences), and determine if there is greater variability in one set relative to the other. Each position with a significant difference in variability between these two sets will be highlighted against a query consensus.

Details:
Entropy has the option of randomizing the combined sequence sets either with replacement or no replacement, and recalculating the entropies for two random data sets broken down into sets of the same size as the original two. If you wish to include sequences of variable length in the alignment, add asterisks (*) to compensate for shorter sequences. Avoid including columns that are all stars. For more details, see explanation of Entropy Options.

Input
Paste your aligned background sequences
[Sample Input]
Or browse for sequence file
Paste your aligned query sequences
[Sample Input]
Or browse for sequence file

Options
Use amino acid class equivalents for the calculation (ONLY for protein sequences)
Calculate the frequency of the most common
aa or nt in each position
Find the statistical confidence using randomization
With replacement Without replacement
Number of randomizations
Number of random samples that can have higher
entropy difference than the actual data

last modified: Tue May 4 10:22 2010


Questions or comments? Contact us at seq-info@lanl.gov.

 
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