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GAP / Glycome Analytics Platform
Offers the opportunity for open source development that integrates multiple web resources into reproducible workflows using Galaxy. The GAP’s integration of glycomics tools into an established bioinformatics web platform to improve their accessibility, usability, re-usability improves the sharing and reproducibility of computational analysis and data in glycomics. Using this platform, users can design in silico workflows to manipulate various formats of glycan sequences and analyze glycomes through access to web data and services.
GRASS / Generation, Ranking and Assignment of Saccharide Structures
Automates elucidation of regular poly- and oligomeric carbohydrate structures. GRASS employs a fast nuclear magnetic resonance (NMR) simulation method for rough ranking against the experimental NMR spectrum. It is based on an accurate simulation method for making refinement. This tool utilizes an incremental scheme with a steric correction parameterized for multiple carbohydrate and non-carbohydrate residues and bond types.
A format based on a connection table approach, instead of a linear encoding scheme, to describe the carbohydrate sequences, with a controlled vocabulary to name monosaccharides, adopting IUPAC rules to generate a consistent, machine-readable nomenclature. The format uses a block concept to describe frequently occurring special features of carbohydrate sequences like repeating units. It exists in two variants, a condensed form and a more verbose XML syntax. Sorting rules assure the uniqueness of the condensed form, thus making it suitable as a direct primary key for database applications, which rely on unique identifiers. GlycoCT encompasses the capabilities of the heterogeneous landscape of digital encoding schemata in glycomics and is thus a step forward on the way to a unified and broadly accepted sequence format in glycobioinformatics.
RINGS / Ressource for Informatics of Glycomes at Soka
Provides algorithmic and data mining tools to aid glycobiology research. RINGS is a freely available Web resource for glycobiologists to analyze their data using the latest data mining and algorithmic techniques. It provides a number of tools including a 2D glycan drawing and querying interface like DrawRINGS, a Glycan Pathway Predictor (GPP) tool for dynamically computing the N-glycan biosynthesis pathway from a given glycan structure, and data mining tools Glycan Miner Tool and Profile PSTMM. RINGS offers free access to these methods for academic research.
A computational approach to automate the sequencing of glycans using metadata-assisted glycan sequencing (MAGS), which combines mass spectrometry analyses with glycan structural information from glycan microarray technology. This approach to computational sequencing of the unknown glycans requires (a) determination of the glycan composition using MALDI-TOF analysis, (b) interrogation of the glycans with lectins and antibodies that bind known determinants, (c) determination of the set of predicted structures based on automated meta-analysis of the experimental data from the virtual glycome database given the constraints of the rules for the biosynthetic pathway of the glycans.
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