I'm fairly new to Biopython, I'm interested in the tool Jce (protein structure alignment by combinatorial extensions) provided @ http://source.rcsb.org/jfatcatserver/ . now the online application works perfectly fine, however I need to implement this tool in my code, possibly using wrappers or python subprocess module. However by my lack of knowledge about these modules i'm unable to find a way to give input to this tool (i.e. two sequences in fasta format and get the output as provided by the tool). can anyone guide me through this? thank you.