QSLiMFinder paper now out. See Edwards Lab: Advanced Access - QSLiMFinder: improved short linear motif prediction using specific query protein data for more details.
Palopoli N, Lythgow KT & Edwards RJ (in press). QSLiMFinder: improved short linear motif prediction using specific query protein data. Bioinformatics 2015; doi: 10.1093/bioinformatics/btv155 [PDF]