UNLABELLED: Scrambled genes are surprisingly common in some species of ciliates. Until now there was no software available to analyze automatically these genes. We present here a program that can automatically align the macronuclear and micronuclear forms of a gene, outputting the location of the macronuclear destined segments and pointer sequences. AVAILABILITY: A web version of the program is available free of charge and can be accessed at http://oxytricha.princeton.edu/GeneUnscrambler.htm

Abstract Summary: Genview and Gencode are tools for testing the adaptive nature of a genetic code under different assumptions about patterns of genetic error and the nature of amino acid similarity. Genview provides a user friendly, point-and-click interface by which a user may reproduce and extend analysis of the adaptive properties of the standard genetic code or any of its secondary derivatives. Genview is a graphical user interface (GUI) program which runs on Linux, Unix®and Microsoft Windows®platforms and is based on the GTK\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(+\) \end{document}toolkit. Genview outputs ASCII configuration files which are interpreted by Gencode to perform an analysis. Gencode is available for the same platforms as Genview. Availability: Online documentation can be found at http://rnaworld.princeton.edu/genview/documentation. The source code can be downloaded from http://rnaworld.princeton.edu/genview/ Contact: [email protected] * To whom correspondence should be addressed.