Abstract
Background The 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 due to their role in chromosomal evolution, genetic disorders and cancer;
Results We present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between two DNA sequences. This computational solution extracts information contents of the two sequences, exploiting a data compression technique, in order for finding 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;
Conclusions Tested 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 complied 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.
List of abbreviations
- AML
- acute myeloid leukemia;
- BAC
- bacterial artificial chromosome;
- CMT
- Charcot–Marie–Tooth;
- CMLS
- Count-Min-Log Sketch;
- CPU
- central processing unit;
- FCM
- finite-context model;
- FISH
- Fluorescence in situ hybridization;
- GB
- gigabyte;
- GGA
- Gallus gallus;
- GHz
- gigahertz;
- HS
- Homo sapiens;
- HSV
- Hue, Saturation, Value;
- HTS
- high-throughput sequencing;
- KB
- kilobyte;
- MB
- megabyte;
- MGA
- Meleagris gallopavo;
- MYA
- million years ago;
- NCBI
- national center for biotechnology information;
- PMP22
- peripheral myelin protein 22;
- PRNG
- pseudo-random number generator;
- PT
- Pan troglodytes;
- RAM
- random access memory;
- Sc
- Saccharomyces cerevisiae;
- Sp
- Saccharomyces paradoxus;
- STMM
- substitution-tolerant Markov model;
- SVG
- Scalable Vector Graphics;
- TST
- ternary search tree;
- UI
- user interface;
- WHS
- Wolf–Hirschhorn syndrome;
- UCSC
- University of California, Santa Cruz.