PGA

The PGA (Peptide identification from RNA-Seq data) software tool addresses the limitation of peptide identification based solely on reference protein databases by proposing a customized protein database generated from RNA-Seq data. The PGA utility, implemented as an R package, offers an end-to-end solution for detecting novel peptides. It automates the processing of tandem mass spectrometry (MS/MS) data from various MS platforms and constructs customized protein databases with or without a reference genome guide. PGA facilitates the identification of novel peptides and generates an HTML-based report with a user-friendly visual interface.

Topic

RNA-seq;Proteomics experiment;Proteomics;Database management;Data integration and warehousing;Data submission, annotation and curation;Data governance

Detail

  • Operation: Deposition;RNA-Seq analysis

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: -

  • Version name: 1.4.0

  • Credit: The International Science & Technology Cooperation Program of China, Chinese National Basic Research Programs, the National High-Tech Research and Development Program of China.

  • Input: Sequence alignment (nucleic acid) [BED] [VCF] [GTF]

  • Output: Protein sequence record [FASTA]

  • Contact: Bo Wen wenbo@genomics.cn ,Shaohang Xu xsh.skye@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq.
  • Wen B, et al. PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. 2016; 17:244. doi: 10.1186/s12859-016-1133-3
  • https://doi.org/10.1186/s12859-016-1133-3
  • PMID: 27316337
  • PMC: PMC4912784

Download and documentation

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