Hi, This question is regarding the netFilter program.
Given a pair of mammalian genomes (e.g. mouse and opossum), I'd like to produce a list of all syntenic regions. This is presumably a combination of the level 1 net with the lower level nets that are syntenic. It has been suggested in the archives that "netFilter -syn" can be used to do this and elsewhere in the archives there's an indication that it has been "tuned" to human-mouse. What does that mean? Will it still work for other mammal pairs? Also, is it possible to specify the permissible gap size? For example, let's say there are two level 1 nets that are separated by a 100bp or less and I want to join them, is that possible with the program? Thanks, Danielle ######################################## Danielle G. Lemay, PhD Postdoctoral Scholar, Bruce German's Lab Food Science and Technology Department University of California at Davis (530) 297 7688 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
