Special factors in biological strings

Biological macromolecules such as DNA, RNA, and proteins can be regarded as finite sequences of symbols (or words) over a finite alphabet. In this pap er, we refer to DNA (RNA) sequences which are words on a four-letter alphab et. A comparison is made between some "genes", or fragments of them, with r andom sequences or random reshuffled sequences on the same alphabet and hav ing the same length. Some combinatorial techniques of analysis of finite wo rds are developed. A crucial role in the comparison is played by the so-cal led special factors of a given word. In all the analysed DNA (RNA) fragment s the distribution on the length of the number of right (left) special fact ors differs, in a very typical way, from the corresponding distribution in a string on the same alphabet and having the same length generated by a ran dom source or obtained by making a random alteration (= shuffling) of the o riginal string. This kind of change is irrespective of the length in the ra nge that we have considered < 2650 bp and of the phylogenetic origin of the fragment. (C) 2000 Academic Press.