Search Results for "proteomic"

The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

Calis-p (The CALgary approach to ISotopes in proteomics) is a java application to estimate isotopic composition (e.g. delta13C or delta15N) of individual species in a microbial community from a proteomic dataset. Calis-p 2.0 handles both natural isotope abundances and data from labelling experiments such as stable isotope probing (SIP). It requires a mzIdent (or target spectrum match) and mzML files as the input and requires about 1 min per mzML file with 10 threads and needs <10 Gb of RAM. It has been tested with data from various nano liquid chromatography/Orbitrap platforms. ...

A tool for extracting and preprocessing spectral count data for label-free quantitative proteomic analysis. This program is designed to be used with the Trans-Proteomic Pipeline (TPP).

Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.

Luciphor is a program that performs phospho-site localization on MS/MS data processed by the Trans-Proteomic Pipeline (TPP). It is the first phospho-site prediction program to provide estimates for the false localization rate (FLR). The program is multithreaded and written in C++ for linux.

ConoSorter is a high-throughput standalone program that implements regular expressions and profile Hidden Markov Models (pHMMs) for large-scale identification and classification of precursor conopeptides into gene superfamilies and classes based on the ER signal, pro-, and mature conopeptide regions generated from raw next-generation transcriptomic or proteomic data. ConoSorter also generates a set of relevant additional information (frequency of protein sequences, length, number of cysteine residues, hydrophobicity rate of N-terminal region) and automatically searches ConoServer database to allow the user to assess the reliability and relevance of the results and to aid the identification of new conopeptide superfamilies and classes.

The JPL project is no longer updated and maintained. It has evolved after being completely reengineered and upgraded. The new project is available at http://mzjava.expasy.org.

BioPlatforms Australia (BPA) has funded a number of datasets generation initiatives around important research themes and scientific challenges faced by Australian researchers to provide a unique public resource for the benefit of Australian life sciences research. These large scale genomic, proteomic and metabolomic datasets are being generated and centrally managed by Bioplatforms Australia in collaboration with leading scientists, research institutes and government agencies. With the support of ANDS, QFAB has developed this web application to enable the publication of these datasets to Research Data Australia (RDA). By login in, BPA can upload ISA-Tab descriptions of their studies and can edit, manage and publish their collection descriptions to Research Data Australia.

ProteoConnections is a bioinformatics platform tailored to address the pressing needs of proteomic analyses. Organise identifications, evaluate the the acquired dataset and accelerate biological interpretation using bioinformatics applications.

Genome Expression Pathway Analysis Tool - Analysis and Visualization of Microarray Gene Expression Data under Genomic, Proteomic and Metabolic Context

A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.)