UNIREP - A MICROCOMPUTER PROGRAM TO FIND UNIQUE AND REPETITIVE NUCLEOTIDE-SEQUENCES IN GENOMES

We present a program UNIREP, written in PowerBASIC for IBM-PCs, that i dentifies repetitive and unique nucleotide sequences in genomes or par ts of genomes. A key feature of the algorithm is an oligonucleotide re presentation in a numerical code to make possible a comparison of all pairs of oligonucleotides (including overlaps) occurring in the analyz ed sequence. This comparison assigns a score to each oligonucleotide, reflecting its similarity/dissimilarity to other oligonucleotides of t he same length in the analyzed sequence. The score is plotted along th e sequence so that peaks in the plot indicate repetitive regions and v ery low values reflect unique sequences. The scores are filtered to su ppress or enhance the unique or repetitive sequences according to the user's wish. UNIREP is extended by auxiliary programs HIGHER and LOWER to list nucleotide sequences that have scores higher or lower than gi ven limits. The potential of UNIREP is demonstrated using several long nucleotide sequences including the complete genomic sequence of EBV.