Question: Generate syntenic blocks between two vertebrates
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gravatar for cmdcolin
22 months ago by
cmdcolin1.1k
United States
cmdcolin1.1k wrote:

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

synteny lastz alignment • 623 views
ADD COMMENTlink modified 22 months ago by wangdp123140 • written 22 months ago by cmdcolin1.1k

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/

ADD REPLYlink modified 20 months ago • written 22 months ago by wangdp123140

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

ADD REPLYlink written 21 months ago by cmdcolin1.1k
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