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The percentage of guanine (G) and cytosine (C) bases within the within the sequence or its selected region, for example:
GC-content("ACGTAC") = ((0 + 1 + 1 + 0 + 0 + 1) / 6) * 100% = 50% |
If the sequence contains degenerate base characters, average values are used, for example:
GC-content("ACGNBCT") = ((0 + 1 + 1 + 1/2 + 2/3 + 1 + 0) / 7) * 100% ~= 59.52% |
In this example "1/2" is used for "N" (any nucleotide), "2/3" us used for "B" (that means "C", "G", or "T" according to the IUPAC nucleotide code).
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Molecular weight for a single-stranded molecule is calculated as a sum a sum of the atomic masses of the molecule compounds:
DNA molecular weight = nA*251.24 + nT*242.23 + nC*227.22 + nG*267.24 + (n-1)*61.97 RNA molecular weight = nA*267.24 24 + nU*244.20 + nC*243.22 + nG*283.24 + (n-1)*61.97 |
Here "nA", "nT", "nC", "nG", "nU" denote the number of the corresponding nucleotide in the molecule, "n" is the number of all bases (61.97 is 97 is the weight of an internal phosphate).
Note that for degenerate base characters average value of nucleotide weight is used, for example, if the sequence also contain "Y" characters (that is "C" or "T"), the sum will include one more summand - "nY*(242.23 + 227.22)/2".
Molecular weight for for a double-stranded molecule is calculated as the sum of the single strands molecular weights.
To calculate the Extinction coefficient, an approach proposed by Richard Owczarzy is used: http://www.owczarzy.net/extinctionDNA.htm. That is for a single-stranded molecule:
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μg/OD260 = nmoleOD260 * molarWeight * 0.001 |
Amino acid sequence common statistics
The following common statistical information is calculated for an amino acid sequence:
- Length
- Molecular weight
- Isoelectic point