myProMS 3.9.3 – Management, Validation and Interpretation of MS-based Proteomic data

myProMS 3.9.3

:: DESCRIPTION

myProMS is a comprehensive bioinformatics environment (database and web server) for management of Mass Spectrometry (MS) protein identification data generated by database-search engines such as Mascot or Sequest. Multiple functionalities are available to mine, validate and interpret the data from both MS and biological point of views. In particular, biological interpretation of the results is facilitated through the use of sophisticated data comparison modules, annotation enrichments and links to external resources. myProMS was designed to optimize data access and sharing during collaboration between users with complementary expertises; typically MS experts and biologists.

::DEVELOPER

Institut Curie, Bioinformatics Core Facility

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsx
Apache
Perl
MySQL
R package

:: DOWNLOAD

myProMS

:: MORE INFORMATION

Citation

Poullet P, Carpentier S, Barillot E.
myProMS, a web server for management and validation of mass spectrometry-based proteomic data.
Proteomics. 2007, 7 (15):2553-6.

DeNovo Pipeline 1.5 – Protein Identification by de novo Interpretation

DeNovo Pipeline 1.5

:: DESCRIPTION

DeNovo Pipeline performes protein identification by de novo interpretation by coupling the PepNovo software for sequencing and the Fasta tool for homology searching.

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ MacOsX / Linux
Java

:: DOWNLOAD

DeNovo Pipeline

:: MORE INFORMATION

EuroForMix 3.3.3 – Statistical DNA Interpretation

EuroForMix 3.3.3

:: DESCRIPTION

EuroForMix is an advanced fully validated open-source, free software used to interpret complex DNA profiles (mixtures) taking into account peak height, stutter and degradation.

::DEVELOPER

EuroForMix team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

EuroForMix

:: MORE INFORMATION

Citation

Pascali VL.
A novel computational strategy to predict the value of the evidence in the SNP-based forensic mixtures.
PLoS One. 2021 Oct 15;16(10):e0247344. doi: 10.1371/journal.pone.0247344. PMID: 34653182; PMCID: PMC8519470.

ANNIE – Protein Sequence Annotation and Interpretation Environment

ANNIE

:: DESCRIPTION

ANNIE is a comprehensive de novo protein annotation system that integrates a large number of indispensable algorithms used in everyday sequence analytic work.

::DEVELOPER

Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W435-40. doi: 10.1093/nar/gkp254. Epub 2009 Apr 23.
ANNIE: integrated de novo protein sequence annotation.
Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G

DrivAER – Identification of driving Transcriptional programs in single-cell RNA sequencing data.

DrivAER

:: DESCRIPTION

DrivAER is a method for identification of Driving transcriptional programs based on AutoEncoder derived Relevance scores. DrivAER infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

DrivAER

:: MORE INFORMATION

Citation:

Simon LM, Yan F, Zhao Z.
DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data.
Gigascience. 2020 Dec 10;9(12):giaa122. doi: 10.1093/gigascience/giaa122. PMID: 33301553; PMCID: PMC7727875.

GlycoPeptideSearch 1.3.12 – Interpretation of N-glycopeptide by searching for Glycopeptide Results consistent with MS/MS spectra

GlycoPeptideSearch 1.3.12

:: DESCRIPTION

GlycoPeptideSearch (or GPS) is a siimplifies data interpretation of N-glycopeptide CID MS/MS datasets by searching for glycopeptide results consistent with MS/MS spectra. Results are tabulated in Excel format.

::DEVELOPER

Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

GlycoPeptideSearch

:: MORE INFORMATION

Citation

J Proteome Res. 2012 Mar 2;11(3):1728-40. doi: 10.1021/pr201183w. Epub 2012 Feb 6.
Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC-MS/MS, and glycan database search.
Pompach P, Chandler KB, Lan R, Edwards N, Goldman R.

PeptideShaker v2.0.33 – Interpretation of Proteomics Identifications from multiple search engines

PeptideShaker v2.0.33

:: DESCRIPTION

PeptideShaker is a search engine independent platform for visualization of peptide and protein identification results from multiple search engines.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux
Java

:: DOWNLOAD

PeptideShaker

:: MORE INFORMATION

Citation

Acta Neurol Scand Suppl. 2012;(195):90-6. doi: 10.1111/ane.12029.
Cerebrospinal fluid proteome comparison between multiple sclerosis patients and controls.
Kroksveen AC, Guldbrandsen A, Vedeler C, Myhr KM, Opsahl JA, Berven FS.

GMS 20140126 – A Turnkey system for Variant Discovery and Interpretation

GMS 20140126

:: DESCRIPTION

GMS (Genome Model System) is an integrated analysis and information-management system.The system borrows concepts from traditional laboratory information-management systems — such as tracking methods and data-access interfaces, — and applies them to genomic analysis. The result is a standardized system that integrates both analysis and management capabilities.

::DEVELOPER

The Genome Institute at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl
R package

:: DOWNLOAD

GMS

:: MORE INFORMATION

MAGI – Mutation Annotation & Genome Interpretation

MAGI

:: DESCRIPTION

MAGI is a publicly available web application to explore and annotate cancer genomics data.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Server

:: DOWNLOAD

MAGI

:: MORE INFORMATION

Citation:

MAGI: visualization and collaborative annotation of genomic aberrations.
Leiserson MD, Gramazio CC, Hu J, Wu HT, Laidlaw DH, Raphael BJ.
Nat Methods. 2015 May 28;12(6):483-4. doi: 10.1038/nmeth.3412.

Synthesis-View – Visualization and Interpretation of SNP Association Results

Synthesis-View

:: DESCRIPTION

Synthesis-View is a data visualization application. Synthesis-View was extended from the previous software “LD-Plus” which also uses a flexible data display format of multiple data “tracks” that can be viewed (Bush, Dudek et al. 2010). Through the use of stacked data-tracks, information on SNP genomic locations, presence of the SNP in a specific study or analysis, as well as related information such as genetic effect size and summary phenotype information, are available for plotting according to user preference.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX
Ruby

:: DOWNLOAD

Synthesis-View

:: MORE INFORMATION

Citation:

Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis.
Pendergrass SA, Dudek SM, Crawford DC, Ritchie MD.
BioData Min. 2010 Dec 16;3:10.