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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
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PoSE: visualization of patterns of sequence evolution using PAML and MATLAB.

Kun Zhao1, Elizabeth Henderson2, Kelley Bullard3

  • 1Polio and Picornavirus Laboratory Branch, G-10, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd., N.E, Atlanta, GA, 30329, USA. kzhao@cdc.gov.

BMC Bioinformatics
|October 23, 2018
PubMed
Summary
This summary is machine-generated.

PoSE (Pattern of Sequence Evolution) offers a user-friendly tool to visualize sequence evolution patterns and phylogenetic signatures. It aids in analyzing nucleotide and amino acid substitutions, providing insights into evolutionary history.

Keywords:
BioinformaticsMATLABMolecular evolutionPAMLPhylogenetics

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Analyzing sequence evolution requires understanding nucleotide and amino acid substitution patterns.
  • Visualizing phylogenetic signatures in aligned sequences presents a significant challenge.

Purpose of the Study:

  • To introduce PoSE (Pattern of Sequence Evolution), a novel resource for visualizing sequence evolution.
  • To facilitate the graphical display of evolutionary history and substitution patterns in sequence alignments.

Main Methods:

  • PoSE utilizes MATLAB scripts integrated with PAML (Phylogenetic Analysis by Maximum Likelihood).
  • It employs an intuitive graphical user interface for ease of use.
  • Substitutions are categorized by type, codon position, and phenotypic effect (synonymous/nonsynonymous).

Main Results:

  • PoSE generates eleven distinct plots to display substitution patterns, including non-synonymous/synonymous ratios (dN/dS).
  • It visualizes inferred substitutions using PAML's baseml or codeml programs.
  • Amino acid substitution patterns can be annotated and inspected within a phylogenetic tree.

Conclusions:

  • PoSE is a valuable tool for identifying major evolutionary patterns in protein-coding sequences and hypervariable regions.
  • It aids in tracking changes in dN/dS ratios.
  • The PoSE resource is publicly accessible for research use.