If you want to get an idea of syntenic blocks between two vertebrates, what would be the best steps?
For example, I have experimented with LASTZ but the aligned pieces are quite small, so a more coarse level overview of synteny is a goal. Should I post process the alignments that LASTZ did using chaining and netting? Is the LASTZ --chain operation good enough? Should I use ucsc pipeline for chaining/netting or any others?
Also is it worth using one-to-one gene mappings as anchors for LASTZ or should you just use the seeding? I don't have a one-to-one mapping currently but could try to find these(?) http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html#fmt_segments
Recommendations other than LASTZ also welcome