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Proteogenomic software tools

Proteogenomics is an area of research at the interface of proteomics and genomics. In this approach, customized protein sequence databases generated using genomic and transcriptomic information are used to help identify novel peptides (not present…
PeptideSieve
Desktop

PeptideSieve

Predicts a peptide’s proteotypic propensity based on its physico-chemical…

Predicts a peptide’s proteotypic propensity based on its physico-chemical properties. PeptideSieve (i) performs an in silico digest of the protein, (ii) converts each of the peptides into chemical…

GAPP
Desktop
proBAMsuite
Dataset

proBAMsuite

Allows to facilitate genome based representation and analysis of proteomics…

Allows to facilitate genome based representation and analysis of proteomics data. proBAMsuite is a bioinformatics framework for proteomics and proteogenomics research. User can browse the cancer…

PGA
Desktop

PGA

An R/Bioconductor package which enables an automatic process for constructing…

An R/Bioconductor package which enables an automatic process for constructing customized proteomic databases based upon RNA sequencing data with or without guidance from a reference genome, searching…

G T A T C G C T A
PROTEOFORMER
Desktop
Web

PROTEOFORMER

A proteogenomic pipeline that delineates true in vivo proteoforms and generates…

A proteogenomic pipeline that delineates true in vivo proteoforms and generates a protein sequence search space for peptide to MS/MS matching. PROTEOFORMER can be combined with canonical protein…

QUILTS
Web

QUILTS Quantitative Integrated Library of Translated SNPs/Splicing

A proteogenomic data integration tool to illustrate protein variant discovery…

A proteogenomic data integration tool to illustrate protein variant discovery using whole genome, whole transcriptome and global proteome datasets generated from a pair of luminal and basal-like…

SpliceVista
Desktop

SpliceVista

A tool for splice variant identification and visualization based on mass…

A tool for splice variant identification and visualization based on mass spectrometry proteomics data. SpliceVista retrieves gene structure and translated sequences from alternative splicing…

sapFinder
Desktop

sapFinder

A program that can use data from public repositories of genetic variants or…

A program that can use data from public repositories of genetic variants or sample-specific next-generation sequencing (NGS) data to automate the generation of variant-containing databases and…

PGx
Web
Desktop

PGx

Supports proteogenomic integration of mass spectrometry proteomics data with…

Supports proteogenomic integration of mass spectrometry proteomics data with next-generation sequencing by mapping identified peptides onto their putative genomic coordinates. PGx represents a useful…

SpectroGene
Desktop

SpectroGene

A software tool for genome annotation using top-down tandem mass spectra.…

A software tool for genome annotation using top-down tandem mass spectra. SpectroGene is a tool for identification using unannotated bacterial genome. SpectroGene could be used for discovery of…

GenomewidePDB
Dataset

GenomewidePDB

A gene-centric proteomic database that integrates proteomic data for proteins…

A gene-centric proteomic database that integrates proteomic data for proteins encoded by chromosomes with transcriptomic data and other information from public databases. GenomewidePDB may not only…

JUMPg
Desktop

JUMPg

Creates multiple databases of DNA polymorphisms, mutations, splice junctions,…

Creates multiple databases of DNA polymorphisms, mutations, splice junctions, partially trypticity, as well as protein fragments translated from the whole transcriptome in all six frames upon RNA-seq…

customProDB
Desktop

customProDB

Enables the easy generation of customized databases from RNA-Seq data for…

Enables the easy generation of customized databases from RNA-Seq data for proteomics search. customProDB bridges genomics and proteomics studies and facilitates cross-omics data integration.

MSProGene
Desktop

MSProGene

Constructs customized transcript databases for tandem mass spectra search.…

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.…

dasHPPboard
Dataset

dasHPPboard

A comprehensive resource to query processed and filtered proteogenomic…

A comprehensive resource to query processed and filtered proteogenomic experimental data from several projects (ENCODE, Illumina Human Body Map 2.0, HPP). dasHPPboard includes results from RNA-Seq,…

PPLine
Desktop

PPLine

A Python-based proteogenomic pipeline providing automated single-amino-acid…

A Python-based proteogenomic pipeline providing automated single-amino-acid polymorphism (SAP), indel, and alternative-spliced-variants discovery based on raw transcriptome and exome sequence data,…

NextSearch
Desktop

NextSearch Nucleotide EXon-graph Transcriptome Search

A proteogenomic pipeline that is based on a nucleotide exon graph. This…

A proteogenomic pipeline that is based on a nucleotide exon graph. This pipeline consists of constructing a compact nucleotide exon graph that systematically incorporates novel splice variations and…

PGTools
Desktop

PGTools

An open source software suite for analysis and visualization of proteogenomic…

An open source software suite for analysis and visualization of proteogenomic data. PGTools is comprised of applications, libraries, customized databases and visualization tools for analysis of…

PoGo
Desktop

PoGo

Uses transcript translations and reference gene annotations to identify the…

Uses transcript translations and reference gene annotations to identify the genomic loci of peptides and post-translational modifications. PoGo is a tool for mapping peptides identified through mass…

PGP
Desktop

PGP

A tool for improving the existing genomic annotations from available proteomics…

A tool for improving the existing genomic annotations from available proteomics mass spectrometry data. As most genome annotation pipelines consist of automated gene finding, they lack experimental…

PG Nexus
Web

PG Nexus Proteomic-Genomic Nexus

A Java-based software package that is designed to integrate genomic and…

A Java-based software package that is designed to integrate genomic and transcriptomic data generated from next-generation sequencing with proteomic data generated from protein mass spectrometry. PG…

ProteoAnnotator
Desktop

ProteoAnnotator

A complete, open source pipeline for proteogenomics which incorporates a…

A complete, open source pipeline for proteogenomics which incorporates a graphical user interface and implements the Proteomics Standards Initiative mzIdentML standard for each analysis stage. All…

GenoMS
Desktop

GenoMS

A proteogenomic approach, GenoMS, that draws on the strengths of database and…

A proteogenomic approach, GenoMS, that draws on the strengths of database and de novo peptide identification methods. Protein sequence templates (i.e. proteins or genomic sequences that are similar…

MINOMICS
Web

MINOMICS

Allows in-depth visualization of prokaryotic transcriptomic and proteomic data…

Allows in-depth visualization of prokaryotic transcriptomic and proteomic data in conjunction with genomics data. MINOMICS generates interactive linear genome maps in which multiple experimental…

PepLine
Desktop

PepLine

A fully automated software which maps MS/MS fragmentation spectra of trypsic…

A fully automated software which maps MS/MS fragmentation spectra of trypsic peptides to genomic DNA sequences. The approach is based on Peptide Sequence Tags (PSTs) obtained from partial…

Peppy
Desktop

Peppy

A software tool designed to perform every necessary task of proteogenomic…

A software tool designed to perform every necessary task of proteogenomic searches quickly, accurately and automatically. The software generates a peptide database from a genome, tracks peptide loci,…

GPF
Desktop

GPF Genomic Peptide Finder

A tool that matches de novo predicted amino acid sequences to the genomic DNA…

A tool that matches de novo predicted amino acid sequences to the genomic DNA sequence of an organism. The matching procedure is error-tolerant to accommodate possible de novo sequencing errors due…

VESPA
Desktop

VESPA

A desktop Java application that integrates high-throughput proteomics data…

A desktop Java application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at…

iPiG
Desktop

iPiG

A tool for the integration of peptide identifications from mass spectrometry…

A tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations. Thereby, the concurrent analysis of proteomic and genomic data is…

Proteogenomic…
Desktop

Proteogenomic Mapping Tool

Provides a standalone application for mapping peptides back to their source…

Provides a standalone application for mapping peptides back to their source genome on a number of operating system platforms with standard desktop computer hardware and executes very rapidly for a…

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