Computer analysis and manipulation of DNA sequences

Abstract

Abstract Programs are described for the efficient analysis of large numbers of DNA sequences for the recurrence of particular short segments. These programs include routines for the determination of oligonucletide frequencies, and for the analysis for perfect and imperfect palindromic sequences with either mirror or two-fold symmetry, as well as for inverted repeat sequences at remote loci. Other routines are included for locating perfect or imperfect matching sequences of any length and of either specified or unspecified sequences in the same or in different molecules. The latter routines are especially useful for locating repeated sequences obscured by random divergence. A number of additional programs are provided for more basic analysis or for cosmetic management of sequences. A routine is included for generating a numbered listing of primary and complementary strands, in selectable order, from an unformatted database. Another routine plots with sequence length the variation in percent G-C or the variation of a particular nearest neighbor or collection of nearest neighbors. Still other routines allow for the determination of translation reading frames and restriction maps.