- Communication -
| In Silico Biology 6, 0024 (2006); ©2006, Bioinformation Systems e.V. |
RANDNA: a random DNA sequence generator
Francesco Piva* and Giovanni Principato
Istituto di Biologia e Genetica, Università Politecnica delle Marche, Via Brecce Bianche, Monte D'Ago, 60131 Ancona, Italy
Email: f.piva@univpm.it, principato@univpm.it
* Corresponding author
Edited by E. Wingender; received January 25, 2006; revised and accepted March 20, 2006; published April 20, 2006
Abstract
Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed.
We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.
Keywords: random nucleotides, entropy, information theory, pseudo-random generator