Proteomics

This section contains links to general proteomics resources, methods, software, and databases. Includes mass spectrometry tools.

Found 45 links

Displaying 15 links

BioMart CentralDatabase Content

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BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. The system also simplifies cross-database searches that might otherwise require several complicated steps.

bioNMFTool Content

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A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

BioSample DatabaseDatabase Content

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The BioSample Database at the EBI is designed to hold information about biological samples, particularly samples referenced from other EBI databases. BioSD data will be exchanged with NCBI

ExPASy Proteomics toolsResource Content

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Various tools for protein identification and characterization, similarity searches, pattern and profile searches, post-translational modification prediction, and more.

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GELBANKDatabase Content

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GELBANK is a database of 2D gel images of proteomes for species with completed genomes. The user can search by sequence description or fragment, or by gel characteristics. Links are made between the sequence and gel when available.

GFSTool Content

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Genome-based Fingerprint Scanning (GFS) takes as input an experimentally obtained peptide mass fingerprint, scans a genome sequence of interest, and outputs the most likely regions of the genome from which the mass fingerprint is derived.

iSARSTTool Content

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iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.

ISOTOPICATool Content

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Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available.

ISPIDER CentralTool Content

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The ISPIDER Central provides a range of services for integrative data analysis in mass spectrometry-based proteomics. It enables users to query multiple proteomic repositories and to add information to proteins retrieved from searches for integrative in silico experiments in proteomics.

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

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Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

MASCOT (Matrix Science)Tool Content

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Protein identification by peptide mass; excellent documentation; incorporates code from MOWSE but allows more search methods on more sequence databases.

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