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 1.4+ which was added as part of Mac OS X 10.3.3.

I've also set up a "Donate" page at the request of some of my favorite users. Please, please visit it!

	Download Sequence Analysis for Mac OS X (Mac OS X 10.3.3 or better)
	Download Sequence Analysis for Windows (Java 1.4.2 or better)
	Download Sequence Analysis for Linux (Java 1.4.2 or better) % java -jar sa.jar -Xms512m -Xmx1024m

What's new in this release

• Updated January 17, 2006 as v1.6.0
  • Fixed launching conflict introduced with QuickTime 7.0.4
  • Digest: Using "REBase 601" enzyme list
  • Allow launching with Java 5 (JDK 1.5)
  • Release History

Starting with version 1.5 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 gilbert@informagen.com.