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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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ACTG: novel peptide mapping onto gene models.

Seunghyuk Choi1, Hyunwoo Kim2, Eunok Paek1

  • 1Department of Computer Science, Hanyang University, Seongdong-gu, Seoul, Korea.

Bioinformatics (Oxford, England)
|December 30, 2016
PubMed
Summary

A new tool, ACTG (Amino aCids To Genome), maps peptide sequences to genomes, accommodating genomic variations like alternative splicing and SNVs. This aids proteogenomic analysis of novel gene products.

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Mapping peptide sequences to genomes is crucial for understanding gene product origins in proteogenomics.
  • Existing tools often require precise genomic positions or exact sequence matches, limiting their utility for novel peptides arising from genomic variations.
  • Structural variations like alternative splicing pose challenges for current peptide-to-genome mapping software.

Purpose of the Study:

  • To develop a novel computational tool for mapping peptide sequences to genome sequences that accommodates various genomic variations.
  • To enable the analysis of novel peptides resulting from complex genomic events, such as alternative splicing and single nucleotide variations.

Main Methods:

  • Developed ACTG (Amino aCids To Genome), a tool that maps peptides to genomes.
  • ACTG considers single exon skipping, junction variations within three edit distances, exon extension, and frame shifts.
  • The tool can integrate single nucleotide variations (SNVs) via VCF files.

Main Results:

  • ACTG successfully maps peptides to genomes while allowing for diverse genomic variations.
  • The tool facilitates the identification and analysis of peptides derived from unannotated or variant gene structures.
  • Integration with VCF files allows for mapping in the presence of SNVs.

Conclusions:

  • ACTG provides a flexible and powerful solution for peptide-to-genome mapping in the presence of genomic variations.
  • The tool enhances proteogenomic studies by enabling the analysis of a broader range of peptide sequences.
  • ACTG supports the discovery of novel gene products and the understanding of their genomic origins.