This chapter notes certain hazards of sequence analysis, including attaching too much significance to discoveries and not being sufficiently cautious about ‘controlling’ experiments for background noise with randomized datasets. Most people do not have an intuitive understanding of randomness and, including ourselves, are susceptible to ‘seeing’ and believing in the existence of patterns in random sequences. This can be a major challenge in DNA sequence analysis. Whether a pattern pops out to the naked eye or is revealed by pattern-seeking software, there is a great risk of misinterpreting the meaning of DNA sequences. Good practices with working with Perl's built-in pseudo-random generating function, rand are provided for generating various types of random sequence including, equally likely proportions, those based on actual ACGT-ratios, and shuffling nucleotides in an original sequence. Side boxes include the topics of DNA binding as a fuzzy and evolved language and making your DNA dice.
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