Sometimes when editing DNA sequences, you wish to highlight specific sequence parts, e.g., all stop codons.
For this, I made an update of the TextMate bundle I wrote for sequence analysis. The new version supports custom highlighting of sequences and can be downloaded from the same location as the old version. There is a new command ("Sequence Analysis" -> "Highlighted Sequences...") for configuring the custom highlighting. It opens a dialog in which you can enter sequence patterns, give each sequence pattern a name and a color, and enable and disable sequence patterns. A sequence pattern can be a single sequence string or a list of multiple sequences separated by dashes ("|"). Unfortunately, you must restart TextMate for the changes to take effect.