Tag: Proteogenomics

VESPA 1.1.1 – Visual Analytics Platform for Exploring Proteogenomics data

VESPA 1.1.1

:: DESCRIPTION

VESPA (Visual Exploration and Statistics to Promote Annotation) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates.

::DEVELOPER

Computational Biology & Bioinformatics, Pacific Northwest National Laboratory

:: SCREENSHOTS

VESPA

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 VESPA

:: MORE INFORMATION

Citation

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.
Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ.
BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.

NeoFlow – Proteogenomics Pipeline for Neoantigen discovery

NeoFlow

:: DESCRIPTION

NeoFlow is a streamlined computational workflow that integrates WES and MS/MS proteomics data for neoantigen prioritization to facilitate cancer immunotherapy.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • R
  • Python

:: DOWNLOAD

NeoFlow

:: MORE INFORMATION

Citation

Wen B, Li K, Zhang Y, Zhang B.
Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis.
Nat Commun. 2020 Apr 9;11(1):1759. doi: 10.1038/s41467-020-15456-w. PMID: 32273506; PMCID: PMC7145864.

PGx – Tool for Proteogenomics Mapping

PGx

:: DESCRIPTION

PGx supports proteogenomic intregration of mass spectrometry (MS) proteomics data with next generation sequencing (NGS) by mapping identified peptides onto their putative genomic coordinates.

::DEVELOPER

Laboratory of Computational Proteomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • Python

:: DOWNLOAD

  PGx

:: MORE INFORMATION

Citation

J Proteome Res. 2015 Dec 7.
PGx: Putting Peptides to BED.
Askenazi M, Ruggles K, Fenyo D.

MSProGene 02 – Integrative Proteogenomics beyond Six-frames and SNPs

MSProGene 02

:: DESCRIPTION

MSProGene is a Java program that constructs customized transcript databases for tandem mass spectra search. RNA-Seq data is used to generate transcripts and to resolve shared peptide protein inference in a proteogenomic network.

::DEVELOPER

MSProGene team

: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 MSProGene

:: MORE INFORMATION

Citation

MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms.
Zickmann F, Renard BY.
Bioinformatics. 2015 Jun 15;31(12):i106-i115.