Related Experiment Video
Updated: Feb 8, 2026

Pattern-based Search of Epigenomic Data Using GeNemo
Published on: October 8, 2017
SOPanG: online text searching over a pan-genome
Aleksander Cislak1, Szymon Grabowski1, Jan Holub2
1Institute of Applied Computer Science, Lodz University of Technology, Lódz, Poland.
Motivation:
The many thousands of high-quality genomes available now-a-days imply a shift from single genome to pan-genomic analyses. A basic algorithmic building brick for such a scenario is online search over a collection of similar texts, a problem with surprisingly few solutions presented so far.
Results:
We present SOPanG, a simple tool for exact pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome. Thanks to bit-parallelism, it achieves pattern matching speeds above 400 MB/s, more than an order of magnitude higher than of other software.
Availability And Implementation:
SOPanG is available for free from: https://github.com/MrAlexSee/sopang.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Related Concept Videos
Genomics
Genomic Imprinting and Inheritance
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
Genome Size and the Evolution of New Genes
Genome Size and the Evolution of New Genes
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
Genomic DNA in Prokaryotes
Genomic Diversity in Bacteria
Although bacterial genomes are much...

