Sprites is a sv caller that specializes in detecting deletion from low-coverage sequencing data. It works by identifying split reads from alignments based on soft-clipping information.
DAFS is a novel algorithm that simultaneously aligns and folds RNA sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment.
GR-Align (GRaphlet-based Aligner) is a fast heuristic procedure for aligning/comparing protein structures according to the Contact Map Opverlap maximization (CMO) paradigm. The algorithm is based on a Needleman-Wunch algorithm where the cost for matching two residues is their graphlet degree similarity.
GR-Align packages contains three software: CMap, DCount, and GR-Align:
CMap converts protein structures (.pdb) files into contact map graphs (leda graphs .gw)
DCount computes the graphlet degree signatures (.ndump files) from Contact Maps
GR-Align aligns protein structures (requieres both contact maps and signatures files)
Graemlin is a tool for aligning multiple global protein interaction networks; Graemlin also supports search for homology between a query module of proteins and a database of interaction networks.