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PeptideSieve

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 property strings, and (iii) computes a likelihood function, which scores the likelihood each peptide is proteotypic. The resulting predictors have the ability to accurately identify proteotypic peptides from any protein sequence and offer starting points for generating a physical model describing the factors.

GAPP / Genome Annotation and global profiling of Posttranslational modifications in Prokaryotes

Validates and refines predicted genetic models and discover diverse post-translational modification (PTM) events. GAPP provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. GAPP enables users to improve genome annotation and identity PTM events from the same experimental proteomic datasets concurrently. This software is a powerful tool for PTM genome annotation and global discovery and is applicable to any sequenced prokaryotic organism.

PGA

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 peptides using MS/MS data, post-processing and generating an HTML-based report with a visualized interface. PGA was evaluated in a data set of the RNA-Seq and proteomic data collected in a human cell line in parallel. Through construction of a customized proteomics database derived from RNA-Seq, PGA was demonstrated as a feasible program for discovering novel peptides arising from genetic variation, alternative splice forms, and novel coding genes.

QUILTS / Quantitative Integrated Library of Translated SNPs/Splicing

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 breast cancer patient derived xenografts (PDX). QUILTS uses protein coding variant calls (germline and somatic) and RNA-Seq based junction predictions to build a customized, tumor specific database containing peptide sequences that contain single nucleotide variants and bridging sequences from alternative splicing against the background of a reference human proteome database.

SpliceVista

A tool for splice variant identification and visualization based on mass spectrometry proteomics data. SpliceVista retrieves gene structure and translated sequences from alternative splicing databases and maps MS-identified peptides to splice variants. The visualization module plots the exon composition of each splice variant and aligns identified peptides with transcript positions. If quantitative mass spectrometry data are used, SpliceVista plots the quantitative patterns for each peptide and provides users with the option to cluster peptides based on their quantitative patterns. SpliceVista can identify splice-variant-specific peptides, providing the possibility for variant-specific analysis. In summary, SpliceVista enables visualization, detection, and differential quantification of protein splice variants that are often missed in current proteomics pipelines.

PGx

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 contribution to the software toolset of any proteogenomics practitioner because it does not impose any mass-informatic on the proteomics branch of the workflow but simply relies on three files summarizing the results of the intermediate sequencing efforts to establish full data integration: a BED file, a FASTA file, and a set of peptides.

MSProGene

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. MSProGene is independent from existing reference databases or annotated SNPs and avoids large six-frame translated databases by constructing sample-specific transcripts. In addition, it creates a network combining RNA-Seq and peptide information that is optimized by a maximum-flow algorithm. It thereby also allows resolving the ambiguity of shared peptides for protein inference.

dasHPPboard

forum (1)
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, Microarrays, Shotgun proteomics and SRM/MRM experiments. The dasHPPboard has been designed as a tool that can be used to share and visualize a combination of proteomic and transcriptomic data, providing at the same time easy access to resources for proteogenomics analyses.

NextSearch / Nucleotide EXon-graph Transcriptome Search

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 a search tool that identifies peptides by directly searching the nucleotide exon graph against tandem mass spectra. NextSearch outputs the proteome-genome/transcriptome mapping results in a general feature format (GFF) file, which can be visualized by public tools such as the UCSC Genome Browser.

PGTools

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 mass-spectrometry data using combined proteomic and genomic backgrounds. A single command is sufficient to search databases, calculate false discovery rates, group and annotate proteins, generate peptide databases from RNA-Seq transcripts, identify altered proteins associated with cancer and visualize genome scale peptide datasets using sophisticated visualization tools.

ProTIE / Proteogenomics Integration Engine

Allows users to identify translated fusions and micro structural variations (microSVs) in matching omics datasets. ProTIE is a standalone software composed of two mains features: (i) MiStrVar, that permits to capture multiple types of microSVs in WGS dataset and (ii) DeFuse, a fusion detection tool. The application also incorporates RNA-Seq evidence to validate expressed microSVs and to detect translated peptides from genomic and transcriptomic aberrations.

PoGo

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 spectrometry to a reference genome to overcome these limitations. It exhibited superior performance over other tools on benchmarking with large-scale human tissue and cancer phosphoproteome datasets. Additionally, extended functionality enables representation of single nucleotide variants, post-translational modifications and quantitative features.

PGP

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 validation of primary structure, having to rely on DNA centric sources of data such as sequence homology, transcriptome mapping, codon frequency, etc. By incorporating the orthogonal set of data, proteogenomics is able to discover novel genes, post-translational modifications (PTMs) and correct the erroneous primary sequence annotations.

PG Nexus / Proteomic-Genomic Nexus

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 Nexus allows users to covisualize peptides in the context of genomes or genomic contigs, along with RNA-seq reads. This is done in the Integrated Genome Viewer (IGV). A Results Analyzer reports the precise base position where LC-MS/MS-derived peptides cover genes or gene isoforms, on the chromosomes or contigs where this occurs. In prokaryotes, the PG Nexus pipeline facilitates the validation of genes, where annotation or gene prediction is available, or the discovery of genes using a "virtual protein"-based unbiased approach.

MINOMICS

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 datasets are displayed together with operon, regulatory motif, transcriptional promoter and transcriptional terminator information. The linear chromosome maps created by MINOMICS provide researchers with a tool to comprehensively mine their experimental data. The tool facilitates documenting this procedure and sharing the results by allowing researchers to export currently displayed genome maps to publication grade images.

Peppy

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, matches peptides to MS/MS spectra and assigns confidence values to those matches. Peppy automatically performs a decoy database generation, search and analysis to return identifications at the desired false discovery rate threshold. Written in Java for cross-platform execution, the software is fully multithreaded for enhanced speed. The program can run on regular desktop computers, opening the doors of proteogenomic searching to a wider audience of proteomics and genomics researchers.

VESPA

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 three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST.

Proteogenomic Mapping Tool

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 variety of datasets. Allowing the selection of different genetic codes for different organisms allows researchers to easily customize the tool to their own research interests and is recommended for anyone working to structurally annotate genomes using MS derived proteomics data.

MSMSpdbb / Multi-Strain Mass Spectrometry prokaryote database builder

Gathers protein databases for prokaryotic organisms. MSMSpdbb is a free standalone software that compiles and clusters various bacterial strains to obtain their complete genomic translations. It aims to generate protein databases intending to detect sequence variations between strains such as single nucleotides polymorphisms (SNPs) and divergent translational start site (TSSs) as well as erase annotation errors and genetic variations among closely related organisms.