AgBase Tools
AgBase provides tools designed to assist with the analysis of proteomics data and tools to
evaluate experimental datasets using the GO.
Functional Analysis Using GO
GOProfiler
Summarizes existing GO annotations for an organism.
GO Annotation Pipeline
These tools may be used independently, or as a pipeline (shown below) to provide GO annotations
for experimental datasets.
GORetriever
Returns AgBase GO annotations for a list of proteins IDs.
GOanna
Allows users to submit a list of protein or nucleotide IDs or a FASTA file containing sequences
and returns AgBase GO annotations based on sequence similarity.
GoSlimViewer
Summarizes GO annotations for datasets using a GO Slim.
Proteomics Analysis
ProtIDer (ESTPlus, PIE Tool) [Available on request]
Enhances proteomics based on EST or EST assemblies by generating databases of matching highly homologous proteins.
The Proteogenomic Pipeline [Available on request]
The Proteogenomic Pipeline provides experimentally-based structural annotations at a complete genome level.
PepFly (Peptide Flyability Prediction) [Available for download]
Constructs a dataset for easy importation into the Weka machine learning toolkit from MS datasets to predict the flyability of peptides.
ProtQuant [Available for download]
ProtQuant is a Java-based tool for label-free protein quantification of Sequest output for the Microsoft Windows environment.