Translation track

If you used MegAlign Pro’s predecessor, MegAlign, you might recall being able to toggle between displaying the alignment as a nucleotide or protein sequence. MegAlign Pro improves upon that functionality by letting you display both versions of the sequence at the same time. You can also choose whether to display a subset of reading frames or all six of them. Displaying the Translation track in MegAlign Pro is especially useful when deciding where to trim an alignment.

To display the Translation track:

Translation tracks in the Sequences view are available only for nucleotide (DNA) sequences, and are dependent on:

• Whether or not tracks are visible in the Sequences view. To display tracks, click on the plus sign next to the sequence of interest.

• Whether or not the Translation box is checked in the Tracks panel. This box is only visible for nucleotide sequences.

Translation track conventions:

• Stop codons are represented by dots.

• For purposes of translation, alignments are assumed to be linear.

• Translations are not displayed for incomplete codons at the right end of the block.

• Translation frames 4-6 are counted from the right end (the 3’ end of the bottom strand).

• In multi-block Mauve alignments, translation is not done across the boundaries of blocks.

To change Translation options:

To learn how to access the options section for this track, see Tracks.

• Use the upper drop-down menu to choose from a variety of NCBI and Lasergene translation codes.

• Put checkmarks next to the reading frames you wish to display, and remove checkmarks from those you do not wish to display. Click All Reading Frames to show or hide all reading frames. Click Top Strand or Bottom Strand to show or hide all the reading frames on that strand.

• Use the left-hand drop-down menu to choose between One-letter or Three-letter amino acid abbreviations.

• Use the right-hand drop-down menu to choose between Uppercase and Lowercase letters.

Click if you wish to return to the default values.