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6.9 years ago
cmdcolin
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3.8k
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
Hi, here is another option for genome alignment in a unit of genes.
Good to try:
http://ec2-52-40-200-174.us-west-2.compute.amazonaws.com/LCGserver/
What pipeline is used to prepare the input for something like this? For example, how do you change your orthologous genes, which are presumably mapped via blasting all proteins against another set of proteins, into the order of the genes on the genome? Thanks for the suggestion though, it has sort of taken me in the new direction of comparing gene order rather than whole genome alignments for synteny