Amino Acid Calculator

Fields

Note

Open Amino Acid Calculator

This opens an Amino Acid Calculator in the Board.

  1. Make the Main Application Window active.
  2. Go to OptionsAmino Acid Calculator.
  3. To make the Amino Acid Calculator window active, click on the Amino Acid Calculator window's Title bar, or click WindowAmino Acid Calculator in the menu of the Board.

Clear

This clears all existing data from the Amino Acid Calculator in preparation for a new usage.

  1. Make the Amino Acid Calculator active in the Board.
  2. Click on AA CalculatorClear.

Create Primers

This designs primers for amplifying ORFs.

  1. Make the Amino Acid Calculator active in the Board.
  2. Enter a DNA sequence in the Genetic Code field.
  3. On the AA Calculator menu click Create Primers.
  4. In the popup, fill in or check/uncheck fields as needed;
    • Min. Primer Length specifies the minimum length of the primers.
    • Max. Primer Length specifies the maximum length of the primers.
    • Min. Tm specifies the minimum calculated melting temperature of the primers and their reverse complements.
    • Max. Tm specifies the maximum calculated melting temperature of the primers and their reverse complements.
    • Tm Calculation is choice of formula for calculation.
      • Simple uses the standard approximation, where Tm = 2 * (#A + #T) + 4 * (#G + #C). # is the 'number of' operator.
      • Not So Simple uses the Simple approximation for sequences shorter than 14 nucleotides, and Tm = 64.9 + 41 * (#G + #C - 16.4) / (#A + #T + #G + #C) otherwise. # is the 'number of' operator.
    • 5' Prefix adds a sequence "prefix" to the 5' end of the primers generated. Prefixes are chosen by name from the dropdown menu. The sequences themselves are stored in Options → Lab Resources → 5' Prefix.
    • 3' Prefix adds a sequence "prefix" to the 3' end of the primers generated. Prefixes are chosen by name from the dropdown menu. The sequences themselves are stored in Options → Lab Resources → 3' Prefix.
    • Limit to 45 Bases limits the length of the primers to 45 bases or less.
    • Skip Start Codon leaves off the ORF start codon from the primer sequence.
    • Skip Stop Codon leaves off the ORF stop codon from the primer sequence.
    • Check for G or C end specifies that primers must have a G or C at each end.
    • Check GC Content 40-60% specifies that primers must have a GC content between 40% and 60%.
    • Check pair Tm difference < 5 specifies that the difference in melting temperature between primer pairs should be less than 5 degrees C.
    • Check for G or C end run > 3 in 5 rejects primers that have 3 or more Gs or Cs in the last 5 bases on each end.
    • Check for runs > 4 rejects primers with stretches of a single nucleotide that are more than 4 bases long.
    • Check for di-nucleotide runs > 4 rejects primers with 4 or more instances of 2 nucleotides in a row.
  5. Click the Create Primers button. If primer creation is possible for the given template sequence and pop-up settings, primers will appear in the 5' Primer and 3' Primer fields, and Tm and length parameters will appear in theirs.

Note

Generate Report for Amino Acid Calculator

This creates a text report for the Amino Acid Calculator.

  1. Make the Amino Acid Calculator active in the Board.
  2. Go to Amino Acid CalculatorGenerate Report for Amino Acid Calculator.

Note

Calculate

This calculates amino acid sequence parameters.

  1. Make the Amino Acid Calculator active in the Board.
  2. Enter amino acid sequence.
  3. Click on the ICON button on the right side of the Amino Acid Sequence field.

Create Mass Spectrometry Profile

This creates an a predicted ESI (ElectroSpray Ionization) mass spectrometry spectrum for a given protein with given 15N, 13C, or SeMet labeling, or a combination of these.

  1. Make the Amino Acid Calculator active in the Board.
  2. Enter amino acid sequence, or genetic code and press the Calculate button ICON to translate it to amino acid sequence.
  3. Click on the ICON button on the right side of the Amino Acid Sequence field.
  4. Set protein labeling using the checkboxes in the Labeled field and quantities in the Occurrence field; the latter are set for natural abundance by default, and can be adjusted set between 0.0 (no labeling) and 1.0 (100% labeling).

Calculate and Translate

This calculates genetic code parameters, translates to amino acid sequence, and calculates amino acid sequence parameters.

  1. Make the Amino Acid Calculator active in the Board.
  2. Enter genetic code.
  3. Click on the ICON button on the right side of the Genetic Code field.

Add Labeling Pattern

This adds a new labeling pattern.

  1. Make the Amino Acid Calculator active in the Board.
  2. Click on the ICON button on the right side of the Labeling Map Field.
  3. A new line will be added to the Labeling Map table, below all previous lines by default, or directly beneath any line that is chosen by clicking on it.
  4. Enter data into the editable columns of the new row.

Note

Delete Labeling Pattern

This deletes an existing labeling pattern

  1. Make the Amino Acid Calculator active in the Board.
  2. Click on the ICON button on the right side of the Labeling Map Field.

View Labeling Pattern

This shows the given labeling pattern in a pop-up window.

  1. Make the Amino Acid Calculator active in the Board.
  2. Click on the ICON button on the right side of the Labeling Map Field.

Note

See also