BioWish: a molecular biology command extension to Tcl/Tk

Thomas Sicheritz-Pontén gif
Dep. of Molecular Biology, University of Uppsala, Sweden
Red text indicates corrections or updates


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 Tcl 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 Tcl are included. Built as a shared library the usage is easy and does not require modification of the Tcl/Tk source code.


BioWish can be obtained from the WWW site The distribution consists of a single C-source file which should compile without modifications on all Unix systems capable of dynamical loading. It requires Tcl 7.5/Tk4.1 Tcl8.0/Tk8.0 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.

BioWish Features


Using BioWish in Tcl scripts requires only a single additional line, a directive to the Tcl intepreter to load the command extension from the shared library, via the load command.
load ./
bio_readfasta ecoli.fas seq
set s [string tolower $seq(sequence)]
puts [bio_seqinfo $s]
for { set nt aaa} {$nt!="aaaaaaa"} {bio_dna_incr nt} {
    puts "$nt = [regsub -all $nt $s {} temp]"
load ./ ;# package require Biowish
biowish::readseq ecoli.fas seq
set s [string tolower $seq(sequence)]
puts [biowish::seqinfo $s]
for { set nt aaa} {$nt!="aaaaaaa"} {biowish::dna_incr nt} {
    puts "$nt = [regsub -all $nt $s {} temp]"
BioWish also includes a sequence editing Tk widget which takes advantage of the extended Tcl commands. (Figure 1).

Figure 1: A screen shot of the Tk sequence editing widget


Ousterhout, 1994
 Ousterhout, J. K. (1994). Tcl and the Tk Toolkit. Addison-Wesley, Reading, MA, USA.

About this document ...

BioWish: a molecular biology command extension to Tcl/Tk

 This document was generated using the LaTeX2HTML translator Version 96.1 (Feb 5, 1996) Copyright © 1993, 1994, 1995, 1996, Nikos Drakos, Computer Based Learning Unit, University of Leeds.

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The translation was initiated by Thomas Sicheritz on Tue Jun 10 09:47:07 MET DST 1997

This work was supported by contract no. BIO4 CT-95-0130 from the European Commission to C. Kurland.

Thomas Sicheritz

Tue Jun 10 09:47:07 MET DST 1997