Abstract

Randomly generated sequences are important in many sequence analysis studies as they represent null hypotheses. There are several existing tools to generate random sequences but each has its own strengths and weaknesses. Building upon the strengths and weaknesses of existing tools, a command?line random sequence generator, RANDOMSEQ, is presented. Generation of random sequences is versatile: (a) fixed or variable length nucleotide or amino acid sequences can be generated; (b) a variety of frequencies for sequence generation is accepted–source sequence, single or n?length nucleotide / amino acid frequencies; (c) generated sequences can be free of user?defined start or stop codons or both; (d) generated sequences can be flanked with randomly selected start and stop codons; and (e) one or more constant regions can exist within the sequence.

Keywords

fixed/variable length, constant random sequence, sequence generator, demonstrating, amino acid, cryptographically, ambiguous nucleotides, operator, versatile method, nucleotides