The transcriptional silencing of one of the female X-chromosomes is a finely 
regulated process that requires accumulation in cis of the long non-coding RNA 
X-inactive-specific transcript (Xist) followed by a series of epigenetic 
modifications. Little is known about the molecular machinery regulating 
initiation and maintenance of chromosomal silencing. Here, we introduce a new 
version of our algorithm catRAPID to investigate Xist associations with a number 
of proteins involved in epigenetic regulation, nuclear scaffolding, 
transcription and splicing processes. Our method correctly identifies binding 
regions and affinities of protein interactions, providing a powerful theoretical 
framework for the study of X-chromosome inactivation and other events mediated 
by ribonucleoprotein associations.