UNIREP: a microcomputer program to find unique and repetitive nucleotide sequences in genomes

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Identifying repetitive and unique nucleotide sequences is crucial for understanding genome organization and function.
• Existing methods may lack efficiency or comprehensive analysis of sequence patterns.

Purpose of the Study:

• To present UNIREP, a PowerBASIC program for IBM-PCs, designed to identify repetitive and unique nucleotide sequences.
• To offer a novel algorithmic approach for analyzing genomic sequences.

Main Methods:

• UNIREP employs an oligonucleotide representation in a numerical code for pairwise sequence comparison.
• A scoring system is implemented to reflect oligonucleotide similarity/dissimilarity within a sequence.
• Scores are plotted to visualize repetitive regions (peaks) and unique sequences (low values), with optional filtering.

Main Results:

• The program successfully identifies and visualizes repetitive and unique nucleotide sequences.
• Peaks in the score plot correspond to repetitive regions, while low values indicate unique sequences.
• Auxiliary programs HIGHER and LOWER facilitate listing sequences based on defined score limits.

Conclusions:

• UNIREP provides an effective computational tool for the analysis of nucleotide sequence composition.
• The program's potential is demonstrated on long nucleotide sequences, including the Epstein-Barr virus (EBV) genome.
• UNIREP offers a user-friendly method for exploring genomic sequence characteristics.