BioWish: a molecular biology command extension to Tcl/Tk

Thomas Sicheritz-Pontén  Dep. of Molecular Biology, University of Uppsala, Sweden thomas@evolution.bmc.uu.se Red text indicates corrections or updates

Introduction

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.

Availability

BioWish can be obtained from the WWW site http://evolution.bmc.uu.se/~thomas/mol_linux 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

• sequence editing: reverse, complement, antiparallel
•  translations
•  sequence statistics
•  G+C content in different positions
•  dna incrementor
•  sequence mutation
•  database searches with BLAST
•  sequence editing widget
•  text editing widget
• graphical open reading frame widget
• sequence conversion via buildin readseq
• contig projects

Usage

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 ./biowish.so
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 ./biowish.so ;# 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

References

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

 

...Sicheritz-Pontén

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

Tue Jun 10 09:47:07 MET DST 1997