Mona Singh • Software

Software (Outdated)

dPUC
dPUC: Domain prediction using context. Download source code.
nCOP
Network coverage of patients: uncover cancer-relevant genes using mutational data in the context of protein interaction networks. Download source code.
DiffMut
Differential mutational analysis---comparing cancer and healthy samples---to uncover cancer-relevant genes from multiple cancer genome samples. Download source code.
DomStratStats
Compute per-protein domain family q-values and local FDRs. Download source code.
Zinc finger specificity prediction
Predict DNA-binding specificities for Cys2His2 zinc finger proteins. Webform.
Concavity
Predict ligand-binding sites from structure. Download source code or use online.
SPICi
A fast, greedy approach for finding dense subnetworks within weighted graphs. Download source code or use online.
Princeton LC-MS/MS Proteomics Data Viewer
Download source code.
Finding maximal exact matches in large sequence data sets using sparse suffix arrays.
Download source code for use within the MUMmer 3 system.
Predicting C2H2 DNA binding sites. Evaluate a C2H2 zinc finger transcription factor for binding to a DNA sequence.
Download or use online.
NetGrep.
Find matches to user-supplied pathway, domain-domain, or other network schema queries. Download or use online.
Side-chain positioning.
Download software to generate LP/IPs for solving the side-chain positioning problem.
MotifSearch.
Search for DNA binding sites, using one of several methods. (Webform and software download.)
Inferring ancestral amino acid content.
Download software to infer ancestral amino acid usage for a set of protein sequences.
bZIP Partner Prediction Program Webpage.
Score potential bZIP coiled-coil protein interactions.
Viral Membrane-Fusion Proteins Program Webpage.
Detect “hairpin” coiled-coil-like structures in viral membrane fusion proteins.
Histidine Kinase Program Webpage.
Analyze putative coiled-coil-like domains in histidine kinases.