Information about Sequence

Statistics about an opened sequence can be found on the Statistics tab of the Options Panel. When a region is selected in the sequence, the statistics are interactively recalculated for this region only. The following information is available:

  • Common statistics (length, molecular weight, etc.) - see the detailed description below
  • Character occurrence
  • Dinucleotide occurrence - available for nucleotide sequences only
  • Codon occurrence - available for nucleotide sequences only
  • Amino acid occurrence - available for nucleotide sequences only

Note that all data displayed on the Statistics tab can be selected with the mouse and copied. Use the copy item in the context menu or a shortcut - Ctrl+C on Windows or Linux, Cmd+C on macOS.

Nucleotide sequence common statistics

The following common statistical information is calculated for a nucleotide sequence:

  • Length
  • GC content
  • Molecular weight
  • Extinction coefficient
  • Melting temperature
  • nmole/OD260
  • μg/OD260

GC content

The percentage of guanine (G) and cytosine (C) bases 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” is used for “B” (which means “C”, “G”, or “T” according to the IUPAC nucleotide code).

Molecular weight

Molecular weight for a single-stranded molecule is calculated as a sum of the atomic masses of the molecule’s components:

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 + 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, and “n” is the number of all bases (61.97 is the weight of an internal phosphate).

For degenerate base characters, the average value of nucleotide weight is used. For example, if the sequence also contains “Y” characters (which are “C” or “T”), the sum will include one more term - “nY*(242.23 + 227.22)/2”.

Molecular weight 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. For a single-stranded molecule:

Extinction coefficient = sum(extinction coefficients of all dinucleotides) - sum(extinction coefficients of inner mononucleotides)

For example, let’s calculate the molar extinction coefficient (“ε”) for “ATGCA”:

ε(ATGCA) = ε(AT) + ε(TG) + ε(GC) + ε(CA) - ε(T) - ε(G) - ε(C)
= 22800 + 19000 + 17600 + 21200 - 8700 - 11500 - 7400
= 53000

As with the other statistics, average values are used in the case of degenerate base characters.

The Extinction coefficient for a double-stranded molecule is calculated as a sum of the extinction coefficients of the two single strands (es1 + es2) multiplied by a coefficient of (1 - hypochromicity h260nm). The hypochromicity effect can be accounted for as follows:

h260nm = (0.287fAT + 0.059fGC)

where _f_AT and _f_GC are fractions of AT and GC base pairs, respectively.

Melting temperature

Click on the gear icon near the Melting temperature label, and the Melting temperature settings dialog will open. Note that UGENE computes Tm for sequence regions from 8 to 10000 bp. Otherwise, an undefined value N/A is output.

See the corresponding page for settings details.

nmole/OD260

The amount of DNA or RNA represented in nanomoles per 1 unit of absorbance at 260 nm dissolved in a 1 ml cuvette with a 1 cm pathlength.

nmole/OD260 = 1000000 / molarExtCoef

μg/OD260

The amount of DNA or RNA represented in micrograms per 1 unit of absorbance at 260 nm dissolved in a 1 ml cuvette with a 1 cm pathlength.

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
  • Isoelectric point
« Details View Melting Temperature »