Software Tools



SNFG Legend Generator

SNFG Legend Generator is a simple web-based tool that generates a Powerpoint file of selected SNFG symbols which can be used for presentations and manuscripts.

   
Processed Data None
Software Type Web-based Software
Availability https://rings.glycoinfo.org/snfg_legend_generator/new
Source code https://git.rings.glycoinfo.org/SNFG/LegendGenerator
License CC-BY-NC
Status Stable, version 1.0
Funding Soka University
Developers Sachiko Akase, Shinichi Higashimoto, Kiyoko F. Aoki-Kinoshita
Contact Kiyoko F. Aoki-Kinoshita: kkiyoko@soka.ac.jp



GRITS Toolbox

GRITS Toolbox is a glycomics MS data processing software. The software allows not just to load, visualize and browser glycomics MS data but also to annotate the data with glycan structures and their fragments. Automatic annotated data can be manually evaluated, changed and exported to Excel. In addition side by side comparison of the different experiment for the study of glycosylation changes and glycosylation expression changes can be performed as well. In addition the software also captures and manages meta data such as sample description and description of the performed experiment.

   
Processed Data MS
Software Type Standalone Software
Availability http://www.grits-toolbox.org
License none
Status stable, continues development
Funding NIH
Future Plans quantification of glycomics data; CMS like methods for glycomics; integration of other data types, such as qRT-PCR
Contact Rene Ranzinger: rene@ccrc.uga.edu



GODESS

NMR spectrum simulation service for carbohydrate-containing molecules (including polymers and glycoconjugates). The output includes signal assignment tables, 1D and multiple 2D spectra. For every simulated chemical shift the predictor reports the expected error, trustworthiness metrics and databases references to data used in the simulation. The software uses empirical approach with own dedicated databases, statistical approach based on CSDB content, and hybrid approach. Supported nuclei are 13C and 1H. Solvent and temperature are taken into account. On the level of structures it supports most structural features of saccharides (several hundred residues, alditols, furanoses, amino acids, fatty acids, sphingoids; glycosidic, amide, or diester linkages). Average accuracy obtained on a large pool of structures was 0.86 ppm for ¹³C and 0.07ppm for ¹H.

   
Processed Data NMR, structures
Software Type web application
Availability http://csdb.glycoscience.ru/database/core/nmrsim.html
License none (free)
Status stable, continues development
Funding Russiann Foundation for Basic Research
Future Plans HMBC prediction, structure iterator & ranking
Contact Phyl Toukach: netbox@toukach.ru



GlycoDigest

GlycoDigest is a tool that simulates the action of exoglycosidases on released oligosaccharides. It has been developed to assist glycobiologists design mixtures of exoglycosidases that can be used to guide the precise determination of glycan structures.

   
Processed Data glycan structures
Software Type Standalone software and integrated in GlycoBase and UniCarbKB
Availability http://www.glycodigest.org
License CC
Status stable, continues development
Funding SIB; National eResearch Collaboration Tools and Resources (NeCTAR) Project
Future Plans Extend range of enzymes for simulation of activity; budding plan with CAZy team.
Contact Matthew Campbell: matthew.campbell@mq.edu.au
Frederique Lisacek: frederique.lisacek@isb-sib.ch



3D structure validation tools (CARP, pdb-care)

Tools for validation of carbohydrate 3D structure data.

   
Processed Data PDB-formatted 3D structures (carbohydrates, glycoproteins, protein-carbohydrate complexes)
Software Type Web application, Integrated in Glycosciences.de
Availability http://www.glycosciences.de/tools
License -
Status stable, continues development
Funding -
Future Plans Include MonosaccharideDB routines for improved handling of modified residues.
Contact Thomas Lütteke: thomas.luetteke@vetmed.uni-giessen.de



Sweet-II

Building of 3D structure models of carbohydrates.

   
Processed Data carbohydrate “sequence” (2D-structure)
Software Type Web application, Integrated in Glycosciences.de
Availability http://www.glycosciences.de/modeling/sweet2
License -
Status stable
Funding -
Future Plans -
Contact Thomas Lütteke: thomas.luetteke@vetmed.uni-giessen.de



GlyProt

In-silico glycosylation of protein 3D structures.

   
Processed Data Protein 3D structure (PDB format), carbohydrate “sequence” (2D-structure)
Software Type Web application, Integrated in Glycosciences.de
Availability http://www.glycosciences.de/modeling/glyprot
License -
Status stable
Funding -
Future Plans -
Contact Thomas Lütteke: thomas.luetteke@vetmed.uni-giessen.de



ISOGlyP (Isoform Specific O-Glycosylation Prediction)

ISOGlyP analizes and roughly predicts isoform specific sites of mucin O-glycosylation for an entered protein sequence . Future goals are to add the long range enhancing effects of remote O-glycosylation and the action of multiple transferases. This work is being performed by a collaboration of Thomas Gerken at Case Western Reserve Univ. (School of Medicine) and Ming-Ying Leung at the Univ. Texas at El Paso (Professor of Mathematical Sci. and Director Bioinformatics Program). The Gerken lab is generating the actual data utilizing a series of unique random (glyco)peptides (refs below) and the Leung lab has developed the web site. We presently have the peptide sequence motif/propensity data for 10 of the 20 isoforms on the site and have generated the remote glycopeptide data on ~11 isoforms (not yet on the site). We also have plans for developing similar approaches to predict the Core 1, Core 3 and sialylation substitution of the peptide GalNAc by similar methods.

   
Processed Data FASTA format protein sequence (manual or file input)
Software Type Web application
Availability http://isoglyp.utep.edu
License none
Status available, under development
Funding NIH (data acquisition and web site 1/2015-11/2018)
Future Plans include remote glycosylation with improved output graphics, add core 1 & 3 and sialylation predictions
Contact T. Gerken: txg2@cwru.edu Tel: 216-368-4556
M. Y. Leung: mleung@utep.edu Tel: 915-747-6836

References:
Perrine et al (2009) http://glycob.oxfordjournals.org/content/19/3/321
Gerken et al. (2011) http://www.jbc.org/content/286/16/14493
Gerken et al (2013) http://www.jbc.org/content/288/27/19900
Kong et al (2015) http://glycob.oxfordjournals.org/content/25/1/55.abstract



GlycReSoft (1)

GlyReSoft is a modular software tool for assigning site specific glycosylation from bottom-up mass spectrometry data sets. The tool accepts LC-MS data from any vendor converted into public data formats and contains modules for following tasks:

   
Processed Data Spectrometry data
Software Type Stand-alone and Web application
Availability https://github.com/GlycReSoft2
License Tentatively Apache2, but always free for academic use
Status Available, Under Development
Funding -
Future Plans -
Contact Joseph Zaia: jzaia@bu.edu

References: Maxwell, E., Tan, Y., Tan, Y., Hu, H., Benson, G., Aizikov, K., Conley, S., Staples, G. O., Slysz, G. W., Smith, R. D., and Zaia, J. (2012) GlycReSoft:A Software Package for Automated Recognition of Glycans from LC/MS Data. PLoS ONE 7, e45474



HS-SEQ (2)

HS-SEQ is a comprehensive algorithm for sequencing of glycosaminoglycan saccharides from activated electron dissociation (ExD) tandem mass spectra. ExD methods encompass ion electron detachment dissociation (EDD) and negative electron transfer dissociation (nETD).

   
Processed Data -
Software Type Stand-alone
Availability https://github.com/hh1985/glycan-pipeline
License -
Status -
Funding -
Future Plans -
Contact Joseph Zaia: jzaia@bu.edu

References: Hu, H., Huang, Y., Mao, Y., Yu, X., Xu, Y., Liu, J., Zong, C., Boons, G. J., Lin, C., Xia, Y., and Zaia, J. (2014) A Computational Framework for Heparan Sulfate Sequencing Using High-resolution Tandem Mass Spectra. Molecular & cellular proteomics : MCP 13, 2490-2502



GlyPy

GlyPy is a modular and extensible library of glycan manipulation tools built in python with minimal dependencies. This library is available for researchers as a resource to solve glyco-bioinformatics problems. All that is required is a minimal knowledge of the general purpose, high level, python programming language. Designed for both batch processing and interactive use. The library includes the following functions:

   
Processed Data -
Software Type Software Library
Availability https://github.com/mobiusklein/glypy
License Tentatively Apache2, but always free for academic use
Status Available, Under Active Development (Feature Requests and Pull Requests Welcome)
Funding -
Future Plans Continued development of glycan structure model and algorithms on that model.
Contact Joseph Zaia: jzaia@bu.edu