Configurable Sequence Highlighting

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.


Finder integration for restoring .svn folders

I created an Automator workflow for the shell script "svnRecover" I wrote about in an earlier post. This allows to restore the .svn folders in a Keynote/Pages or similar document that is under Subversion control. For this, you simply select More->Automator->SVN_Recover from the document's context menu (see screenshot). You can download the automator workflow here. To install it, unzip it and copy the workflow document into the folder ~/Library/Workflows/Applications/Finder in your home directory. (You do not need to install the shell script separately; it is included in the Automator workflow.)

Update 2008-09-16: I fixed a bug that could lead to the deletion of all contents of folders with extended privileges.


DNA Sequence Analysis with TextMate

I have built my first bundle for TextMate, the famous text editor for Mac OS X. The bundle allows simple DNA sequence analysis tasks, like setting the reading frame, sequence comparison, expressing codons, and determining masses of the expressed amino acids. For sequence comparison, I integrated two tools from EMBOSS: needle and water. These are also accessible via a web interface of the European Bioinformatics Institute.

You can download the bundle here. Just unzip the file and double click it or drag it on the TextMate application. When you edit a sequence file you should select "Fasta" as language at the bottom of TextMate. Then, you can access the sequence analysis commands by pressing Ctrl+Escape.

Have fun!