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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
Or browse for sequence file
Paste your aligned query sequences
Or browse for sequence file

Options
Amino acid class equivalents Use equivalents based on chemical similarity for the calculation (ONLY for protein sequences)
Frequency Calculate the frequency of AA or NA at each position
Randomization Calculate the statistical confidence using randomization
With replacement Without replacement
 # of samples
 # of samples having higher entropy difference than the actual data. Cutoff for conserved signature
N-linked glycosylation sites Treat potential N-linked glycosylation sites separately using 'O' (ONLY for protein sequences)
Non-standard AA or NT characters
(ambiguity codes, #, ?, etc.)
Include in the calculation as different states
Exclude
Limit region Calculate within the region between and

last modified: Mon Feb 24 11:27 2020


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

 
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