Bioinformatics Software Applications

The Bioinformatics and Computational Biosciences Branch creates applications prepared by NIAID researchers and collaborators to share with the broader research community.

Web Applications

Examples of web applications include the following:

Hemagglutinin Structure Prediction (HASP) Server
HASP is an interactive tool for the generation and analysis of high-quality hemagglutinin (HA) homology models.

PaVE: Papillomavirus Episteme
PaVE is a bioinformatics resource for papillomavirus researchers. PaVE includes over 420 complete genomic sequences from the Papillomaviridae and will soon feature tools for the comparative analysis of viral isolates. PaVE includes unique visualization and search tools for sequence information specific to the Papillomaviridae.

DRAP uses an automated workflow to read dosage-plate layout files and experimental data from plate readers, construct non-linear dose-response curves, determine IC50 and IC90 for each treatment, and generate analysis reports with publication-quality images.


The NIAID Office of Cyber Infrastructure and Computational Biology, Bioinformatics and Computational Biosciences Branch is developing a web application, Nexplorer3, using a semantic web framework for visually manipulating comparative data in CDAO format and extracting biologically significant results based on reasoning.

SNP Explorer
SNP Explorer is used for the visualization and analysis of SNPs from custom Affymetrix resequencing Hyper-IgM/CVID microarrays.


Desktop Applications

The following are examples of downloadable desktop applications:

NetCirChro: Networks on Circular Chromosome (Cytoscape plug-in)
NetCirChro allows researchers to view and analyze network data in a context of chromosomal location and proximity. NetCirChro is particularly useful to any researcher studying bacterial genomes. Researchers can take advantage of the synchronization between Cytoscape and the NetCirChro plug-in to perform complex analyses, searches, and selections that were not possible before the NetCirChro tool was available.

SPICE: Simplified Presentation of Incredibly Complex Evaluations
The SPICE application is used by immunologists for data mining and visualization of multicolor flow cytometry data. However, the application has a broader utility: researchers may use SPICE to analyze any multivariate data set that has a series of nominal measurements and a single continuous measurement.

dCAS: Desktop cDNA Annotation System
The dCAS software automates large-scale cDNA sequence analysis. Researchers import their raw cDNA sequences to the dCAS software, which then automatically performs a series of clean-up steps and analyses. It then outputs an annotated Microsoft Excel file with assemblies.

Contact Information

For more information on Bioinformatics Software Applications, email
Bioinformatics and Computational Sciences Branch


    Content last reviewed on February 16, 2011