ArticleGigaScience2020
Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 18 citations in OpenAlex.
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- A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules.Briefings in functional genomics · 2025Article
- Bioinformatics tools for the sequence complexity estimates.Biophysical reviews · 2023Review
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- AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.GigaScience · 2022Article
- The complexity landscape of viral genomes.GigaScience · 2022Article
- The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features.GigaScience · 2022Article
- Genome and Methylome analysis of a phylogenetic novelMicrobial genomics · 2021Article
- AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models.Entropy (Basel, Switzerland) · 2021Article
- Efficient DNA sequence compression with neural networks.GigaScience · 2020Article
- Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements.GigaScience · 2020Article
- The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances.PloS one · 2020Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial owing to their role in chromosomal evolution, genetic disorders, and cancer.
resultsWe present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between 2 DNA sequences. This computational solution extracts information contents of the 2 sequences, exploiting a data compression technique to find rearrangements. We also present Smash++ visualizer, a tool that allows the visualization of the detected rearrangements along with their self- and relative complexity, by generating an SVG (Scalable Vector Graphics) image.
conclusionsTested on several synthetic and real DNA sequences from bacteria, fungi, Aves, and Mammalia, the proposed tool was able to accurately find genomic rearrangements. The detected regions were in accordance with previous studies, which took alignment-based approaches or performed FISH (fluorescence in situ hybridization) analysis. The maximum peak memory usage among all experiments was ∼1 GB, which makes Smash++ feasible to run on present-day standard computers.
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