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S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences.

Laurynas Kalesinskas1,2, Evan Cudone1,3, Yuriy Fofanov4

  • 1Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.

Evolutionary Bioinformatics Online
|September 25, 2018
PubMed
Summary
This summary is machine-generated.

S-plot2 enhances genomic comparison by visualizing nucleotide usage similarities and dissimilarities. This tool aids in identifying lateral gene transfer (LGT) and evolutionary divergence across diverse species.

Keywords:
alignment-freecomparative genomicsgene lossgene transfer

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Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative genomics

Background:

  • Comparative genomics requires efficient tools to analyze vast amounts of sequencing data.
  • Identifying genomic dissimilarities is crucial for understanding gene transfer, loss, gain, and selection.
  • Previous software, S-plot, utilized an alignment-free approach for bacterial genome comparison.

Purpose of the Study:

  • To introduce S-plot2, an advanced software for interactive genomic sequence comparison.
  • To expand upon S-plot's capabilities by incorporating new analytical metrics and features.
  • To demonstrate S-plot2's utility in analyzing both microbial and eukaryotic genomic data.

Main Methods:

  • S-plot2 generates interactive 2D heatmaps based on nucleotide usage similarities and dissimilarities.
  • The software includes enhanced analytical metrics, reporting options, and integrated BLAST functionality.
  • It is capable of analyzing partial or complete genomes, including large eukaryotic chromosomes.

Main Results:

  • S-plot2 effectively visualizes genomic similarities and dissimilarities, aiding in the identification of key genomic events.
  • Case studies demonstrated its application in identifying strain-specific lateral gene transfer (LGT) in *Pseudomonas aeruginosa*.
  • Analysis of human, chimpanzee, and rhesus macaque autosomes revealed lineage-specific divergence contributions.

Conclusions:

  • S-plot2 offers a powerful, versatile platform for visual and quantitative comparison of nucleotide sequences.
  • The tool facilitates the investigation of molecular divergence rates and evolutionary events across various genomic scales.
  • S-plot2 is a valuable resource for comparative genomic studies, available for Linux and MS Windows.