Smash plus plus : an alignment-free and memory-efficient tool to find genomic rearrangements

Show full item record



Permalink

http://hdl.handle.net/10138/316325

Citation

Hosseini , M , Pratas , D , Morgenstern , B & Pinho , A J 2020 , ' Smash plus plus : an alignment-free and memory-efficient tool to find genomic rearrangements ' , GigaScience , vol. 9 , no. 5 , 048 . https://doi.org/10.1093/gigascience/giaa048

Title: Smash plus plus : an alignment-free and memory-efficient tool to find genomic rearrangements
Author: Hosseini, Morteza; Pratas, Diogo; Morgenstern, Burkhard; Pinho, Armando J.
Contributor: University of Helsinki, Department of Virology
Date: 2020-05
Language: eng
Number of pages: 15
Belongs to series: GigaScience
ISSN: 2047-217X
URI: http://hdl.handle.net/10138/316325
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 owing 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 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. 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 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 similar to 1 GB, which makes Smash++ feasible to run on present-day standard computers.
Subject: genomic rearrangement
alignment-free
genome comparison
genome duplication
data compression
information theory
probabilistic-algorithmic model
complexity
visualization
high-throughput sequencing
LARGE NUMBERS
COMPRESSION
SEQUENCE
3111 Biomedicine
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
giaa048.pdf 3.936Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record