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Sequence Analysis

This (Java) application is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant. These clients have graciously allowed me to release these works into the public domain as freeware for Macintosh OS X in order to promote the platform and to encourage migration from Classic.

The upper window panel can hold several sequences, which are both editable and selectable. The tabs in the lower analysis panel try to keep up with the current sequence selection to provide immediate feedback. The selection is used in some modules as only the portion being analyzed for other modules i.e. Digest is used to determine if enzymes cut in the in or outside of the selection.

Most commonly available sequence formats have been reverse engineered. You can also access a sequences from the NCBI via its GID or UID. This currently cannot be done from behind a firewall.

Most of the analyses are simple enough that they are obvious to use, Composition, pI. Others could stand some documenation i.e. Pairwise and Primer Design. The Publish tab uses a string to control the layout. Click on the Legend button for some help.

This release of Sequence Analysis, requires Java 1.5+.

Macintosh Download for Mac OS X, for Java 7 (Mountain Lion & Mavericks)

After downloading you may have to go the 'Security & Privacy' System Preferences and

  • Click on the 'General' tab
  • Unlock the panel in the lower left corner
  • Select the 'Anywhere' option for 'Allow applications downloaded from:'
  • Launch and quit'Sequence Analysis'
  • Return the 'Allow applications downloaded from:' option to its original selection for your own security

Mavericks (Mac OSX v10.9) my remove or disable your existing Java installation. When launching Sequence Analysis you may get a "JRELoadError" error message. In this case, the first thing to try is (re)installing Java from the Oracle Java Download page.

Macintosh Download for Mac OS X, up to Java 5
Macintosh Download for Mac OS X v10.5

What's new in this release

Starting with v1.5 the Pairwise module is using the NeoBio Pairwise Alignment Library written by Sergio Anibal de Carvalho Junior. Please visit his web site for more details on the algorithms used. He has made his Java source available use with a very generous License which allowed me incorporate it into Sequence Analysis. He is accepting donations for his work via SourceForge.

Also incorporated into version 1.0.9 of MRJAdapter by Steve Roy which gives this Java application the very nice look of a native Mac OS X application.

Easter Egg: double click a "green" ORF in the Open Reading Frame tab and new protein will be created.

Send constructive comments directly to me at