BioWish: a molecular biology command extension to Tcl/Tk

Abstract

The Tcl/Tk (Ousterhout, 1994) scripting language has proved to be a powerful tool for building programs involved in the analysis of molecular sequence data. However, typical 'biological' operations, like the translation of a nucleotide sequence to the corresponding amino acid sequence, or the calculation of the G + C content in different codon positions in a 50 kbp cosmid sequence, are performed far too slowly with the standard Tel commands. To circumvent this problem, we have constructed a library that extends the Tcl/Tk language by adding primitive operators suited for sequence analysis implemented in the C-language. Additional commands related to molecular biology, written in Tel, are included. Built as a shared library, usage is easy and does not require modification of the Tcl/Tk source code. BioWish can be obtained from the WWW site http://evolution.bmc.uu.se/~thomas/moLlinux. The distribution consists of a single C-source file which should compile without modifications on all Unix systems capable of dynamical loading. It requires Tel 7.5/Tk4.1 or higher. No patching of the Tcl/Tk core is required. On systems where dynamic loading is not available, BioWish can be compiled as a standalone Tk intepreter.