Tools
Other specialized Software Tools & Technologies
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NCBI provides several tools for downloading custom data sets. This page provides the option to download the software.
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For Description of uLIPSTIC Software, see this article. This software is described as recording cell-cell interaction. See the publication.
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PacBio sequencing technology has evolved to a different type of long read, known as highly accurate long reads, or HiFi reads. READ MORE for this 'Method of the year'
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Next-generation protein sequencing (NGPS) revolutionizes the comprehensive identification of all protein species within a single biological organism. READ MORE. Also, see here.
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For more accurate structure prediction of biomolecular interactions, one can use AlphaFold 3. However, not revealing the code has made it less useful for further research; See GEN article. Also see, OpenFold, a fast, memory efficient, and trainable implementation of AlphaFold 2.
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For other technologies, see here
Tools for Glycobioinformatics
Following is the list of commonly used specialized software tools for Glycan Analysis. For the benefit of the researchers, list of tools is also provided for MS data analysis (MS tools), NMR data analysis (NMR tools, 3D Modeling & Simulation (Model), and other specialized tools (special tools; see: Publication, chapter 16 (page 323-375), for a short description)
BIONIC
For Glycopeptide identification, a Proprietary software (see: PMID: 23255153)
CARTOONIST
For MS analysis of glycan structure, a standalone tool software (see: Yu, CY., et. al., 2013)
EMNGly
For predicting N-linked glycosylation sites using the language models for feature extraction. (see the publication)
GAGfinder
MS analysis specifically for GAGs, A standalone softwar (see: PMID: 29615495)
GAG-ID
MS analysis of heparin/heparan sulfate, a standalone software (see: PMID: 25887393)
GLYCOFOREST
LC-MS analysis of glycan, a standalone tool (see: Glycoforest 1.0)
GLYCOFRAGMENT
For MS analysis of glycan A part of glycosciences.de portal (see: Ref)
GLYCOANALYZER
Automated glycan annotation software from MS analysis data, a standalone software (see: PMID: 22903841)
GLYCOGENIUS
A High-throughput Glycan Composition Identification Tool (Loponte, HF, et al., 2025)
GLYCOUNTER
An informative tool for extracting glycan related information from MS data (Kothlow, et. al., 2025)
I-GPA, Integrated GlycoProteome Analyzer
for Automated Identification and Quantitation of Site-Specific N-Glycosylation (Park, GW et. al., 2016)
Other Useful Tools
BRENDA
A Comprehensive Enzyme Information system; also provides structure-based search function.
GRITS Toolbox
A platform for glycomics data processing and archiving.
RHEA
It is an expert-curated knowledgebase of chemical and transport reactions of biological interest.