Standalone Software

Disease Pathfinder

Category: Systems Biology/Interactomics
Website: contact PI
Platform: Linux - C/C++
PI: Gurkan Bebek
Reference: Patel VN, Bebek G, Mariadason JM, Wang D, Augenlicht LH, Chance MR. Prediction and testing of biological networks underlying intestinal cancer. PLoS One. 2010 Sep 1;5(9). pii: e12497.

Disease PathFinder returns candidate pathway segments connecting dissease associated genes of interest with possible missing links (recovered false negatives).

Integrated Network Similarity Pipeline (INSPIrE)

Category: Systems Biology/Interactomics
Website: contact PI
Platform: Linux - C/C++
PI: Gurkan Bebek

INSPIrE performs quantitative within-species global network alignment. INSPIrE finds the topologically optimum alignment of genes/proteins using protein domain information from pfam and protein function information from gene ontology.

SEquence ALignment evaluation suite (SEAL)

Category:Next Generation Sequencing
Website: http://compbio.case.edu/seal/
Platform: Java
PI: Mehmet Koyuturk
Reference: Ruffalo M, LaFramboise T, Koyuturk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics. 2011 Oct 15;27(20):2790-6. Epub 2011 Aug 19.

SEAL is a comprehensive sequencing simulation and alignment tool evaluation suite. This software provides several utilities that can be used to evaluate alignment algorithms, including generating synthetic genomes, reading pre-existing genomes, simulating sequencing reads, applying alignment tools to these reads and measuring the accuracy of alignment tools when run on this data.

LOgistic regression tool for calibrating the QUality of short read Mappings (LoQuM)

Category: Next Generation Sequencing
Website:http://compbio.case.edu/loqum/
Platform: R/Python
PI: Mehmet Koyuturk

LoQuM is a machine learning tool that recalibrates short read mapping quality scores. The mapping quality scores provided by alignment tools do not strongly correlate with actual mapping accuracy. LoQuM uses additional information from reads and their alignment statistics to provide mapping quality scores that more closely represent actual mapping accuracy.