Bioinformatics Advance Access originally published online on January 29, 2004
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Bioinformatics 20(5) © Oxford University Press 2004; all rights reserved.
Applications Note |
In silico analysis of complete bacterial genomes: PCR, AFLP–PCR and endonuclease restriction
Department of Immunology, Microbiology and Parasitology, University of the Basque Country, Paseo de la Universidad, 7, 01006 Vitoria-Gasteiz, Spain
Received on September 4, 2003
; accepted on October 24, 2003
Advance Access Publication February 5, 2004
Summary: We have developed a website, www.in-silico.com, which runs a software program that performs three basic tasks in completely sequenced bacterial genomes by in silico analysis: PCR amplification, amplified fragment length polymorphism (AFLP–PCR) and endonuclease restriction. For PCR, after selection of the genome and introduction of primers, fragment size, DNA sequence and corresponding open reading frame (ORF) identity of the resulting PCR product is computed. Plasmids of sequenced species may be included in the analysis. Theoretical AFLP–PCR analyzes similar parameters, and includes a suggestion tool providing a list of commercial restriction enzyme pairs yielding up to 50 amplicons in the selected genome. Endonuclease restriction analysis of complete genomes and plasmids calculates the number of restriction sites for endonucleases in a given genome. If the number of fragments is 50 or fewer, pulsed field gel electrophoresis image and restriction maps are illustrated. Other tools that have been included in this site are ORF search by name and DNA to protein translation as well as restriction digestion of user-defined DNA sequences.
Availability: This is a new molecular biology resource freely available over the Internet at http://www.in-silico.com
Contact: oipbibij{at}lg.ehu.es
* To whom correspondence should be addressed.
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