PMID- 32432328
OWN - NLM
STAT- MEDLINE
DCOM- 20211004
LR  - 20240328
IS  - 2047-217X (Electronic)
IS  - 2047-217X (Linking)
VI  - 9
IP  - 5
DP  - 2020 May 1
TI  - Smash++: an alignment-free and memory-efficient tool to find genomic 
      rearrangements.
LID - 10.1093/gigascience/giaa048 [doi]
LID - giaa048
AB  - 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  approximately 1 GB, which 
      makes Smash++ feasible to run on present-day standard computers.
CI  - (c) The Author(s) 2020. Published by Oxford University Press.
FAU - Hosseini, Morteza
AU  - Hosseini M
AD  - IEETA/DETI, University of Aveiro, Campus Universitario de Santiago, 3810-193 
      Aveiro, Portugal.
FAU - Pratas, Diogo
AU  - Pratas D
AD  - IEETA/DETI, University of Aveiro, Campus Universitario de Santiago, 3810-193 
      Aveiro, Portugal.
AD  - Department of Virology, University of Helsinki, Haartmaninkatu 3, 00014 Helsinki, 
      Finland.
FAU - Morgenstern, Burkhard
AU  - Morgenstern B
AD  - Department of Bioinformatics, University of Gottingen, Goldschmidtstr. 1, 
      37077 Gottingen, Germany.
AD  - Gottingen Center of Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 
      37077 Gottingen, Germany.
FAU - Pinho, Armando J
AU  - Pinho AJ
AD  - IEETA/DETI, University of Aveiro, Campus Universitario de Santiago, 3810-193 
      Aveiro, Portugal.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Gigascience
JT  - GigaScience
JID - 101596872
SB  - IM
MH  - Algorithms
MH  - Computational Biology/*methods
MH  - Gene Rearrangement
MH  - Genome
MH  - Genomics/*methods
MH  - High-Throughput Nucleotide Sequencing
MH  - Sequence Analysis, DNA/methods
MH  - *Software
PMC - PMC7238676
OTO - NOTNLM
OT  - alignment-free
OT  - complexity
OT  - data compression
OT  - genome comparison
OT  - genome duplication
OT  - genomic rearrangement
OT  - high-throughput sequencing
OT  - information theory
OT  - probabilistic-algorithmic model
OT  - visualization
EDAT- 2020/05/21 06:00
MHDA- 2021/10/05 06:00
PMCR- 2020/05/20
CRDT- 2020/05/21 06:00
PHST- 2020/01/11 00:00 [received]
PHST- 2020/04/06 00:00 [revised]
PHST- 2020/04/20 00:00 [accepted]
PHST- 2020/05/21 06:00 [entrez]
PHST- 2020/05/21 06:00 [pubmed]
PHST- 2021/10/05 06:00 [medline]
PHST- 2020/05/20 00:00 [pmc-release]
AID - 5841055 [pii]
AID - giaa048 [pii]
AID - 10.1093/gigascience/giaa048 [doi]
PST - ppublish
SO  - Gigascience. 2020 May 1;9(5):giaa048. doi: 10.1093/gigascience/giaa048.