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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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GPAC-genome presence/absence compiler: a web application to comparatively visualize multiple genome-level changes.

Angela Noll1, Norbert Grundmann2, Gennady Churakov3

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Molecular Biology and Evolution
|September 28, 2014
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Summary

Researchers developed a new tool for large-scale comparative genomics, enabling simultaneous analysis of thousands of genomic loci across species. This tool facilitates the study of gene evolution and the presence or absence of genomic sequences.

Keywords:
GPACUCSC Genome Browserexonsintronsmultilocus genome comparisonnumtspresence/absence visualizationretroposons

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Area of Science:

  • Comparative Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • The University of California Santa Cruz (UCSC) Genome Bioinformatics Department provides valuable genome-wide and comparative sequence data.
  • Current UCSC tools allow visualization of orthologous genomic loci in a single locus, limiting large-scale comparative analyses.
  • Analyzing presence/absence patterns of genomic sequences across species is crucial for understanding gene and genome evolution.

Purpose of the Study:

  • To introduce a novel tool for parallel analysis of thousands of genomic loci for cross-species presence/absence patterns.
  • To enable large-scale comparative analyses that were previously not feasible with single-locus visualization.

Main Methods:

  • Development of a genome presence/absence compiler tool.
  • Utilizes multiway genome alignments and annotated coordinates of genomic locations.
  • Presents presence/absence patterns in a flexible, color-coded table linked to UCSC Genome Browser alignments.

Main Results:

  • The tool facilitates the simultaneous comparison of thousands of genomic loci.
  • Enables the study of diverse evolutionary questions, including gene gain/loss, novel elements, and viral particles.
  • Demonstrates versatile information content for analyzing elements like 7SL-derived transposed elements, nuclear mitochondrial DNA, DNA transposons, and miRNAs in primates.

Conclusions:

  • The presented tool is the first to facilitate parallel analysis of thousands of genomic loci for cross-species presence/absence patterns.
  • This approach significantly enhances the ability to conduct large-scale comparative genomic studies.
  • The tool provides valuable insights into genome evolution and the distribution of various genomic elements across species.