• Translating DNA sequence to protein
  • Choose the Protein | Translation command to open the Translation Parameters dialog box. You may choose necessary options to display translation results.

    1) Amino Acid symbol

    You may select One letter or Three letter code for amino acids.

    2) Reading Frame

    You may choose Reading Frame 1, Frame 2 and Frame 3..

    You may also choose the All option to translate the DNA sequence in all six reading frames (including three frames of the minus strand).

    3) Annotations

    If there are annotations in the sequence, you have the options to deal with them.

    1. Excluding some or all annotations. Choose the Exclude option and select one or more annotations. DNAMAN will translate all sequence except the regions defined in selected annotations.
    2. Using only some or all annotations. Choose the Use only option and select one or more annotations. DNAMAN will translate only the sequence regions defined in selected annotations.
    3. Including all annotations. Do not select any of the annotations. DNAMAN will translate all sequence regardless of annotations.

    4) AA per line

    You may define the number of amino acids of each line in the output result.

    5) Show DNA

    DNAMAN may show Single strand or Double starnd DNA sequence together with amino acid sequences. You may also choose not showing DNA sequence.

    6) Resulting AA sequences to channel option

    If further analysis of amino acid sequences is required, you may direct the amino acid sequences to channels.

    If IUPAC code resent in the default DNA sequence and the coding amino acid is undefined, “X” may appear in that position.

    DNAMAN can translate a part of the default DNA sequence to amino acid sequence. You may define the analysis region, such as an open reading frame, for translation. Choose the Sequence | Current Channel | Analysis Definition command to specify the region you want to analyze. Then choose the translation command to display the results.

    1     CTAAAGAAACATCTGAGGTGGTTAAAAGCTCTCCCTCGTGTCACCCCCTTTTATGCAGTCAAATGTAATGATAGCAAAGCCAAGACGAAG
    91    ACGAGAGAATGACAAAACACTCATGTATTACGGGAATGATGGTGTCTATGGATCGTTCAATTGCATCTTGTATGATCATGCACATGTTAA
    1              M  T  K  H  S  C  I  T  G  M  M  V  S  M  D  R  S  I  A  S  C  M  I  M  H  M  L  N
    181   ACCAGTTCTGCAAAAGCGGCCTAAACCAGATGACGGCTGCTACTCCTGCAGCATATGGGGCAACGGATTCCAGAGGCCAACAATACATTA
    29       Q  F  C  K  S  G  L  N  Q  M  T  A  A  T  P  A  A  Y  G  A  T  D  S  R  G  Q  Q  Y  I  M
    271   TGCGATGCTCCTGTGCCTGTGAAAGTGGAATTGAGTATCCAGCAACTTGTGCTTCAGCTAGTATTAATGTATAAATAATAAATACTTAGA
    59       R  C  S  C  A  C  E  S  G  I  E  Y  P  A  T  C  A  S  A  S  I  N  V  *
    361   AACTAACTGCAAGTTTAGTCATTGAATTTAGGGCATTTGGGGGACCATTAACTTAATTCTTGCTAGAATTTTTTAAGTGTTTTTTTAAAA
    451   GTTTAGGTTTGGCATAAACACGACAAAAAA

    The above example shows a DNA sequence and the translated amino acid sequence. There are three methods for further analysis of the protein sequences. In the Translation Parameters dialog box:

    1. Choose the Resulting AA sequences to channel No option. Amino acid sequences will be loaded directly to channels for analysis.
    2. Select one of the three reading frames (not All), and not check the Display with DNA sequence option. The resulting text file will be formatted and can be directly used for analysis. Save this file and load it into a sequence channel as protein sequence.
    3. Alternatively, you may select the sequence and load the selection using the Sequence | Load Sequence | From Selection menu.