[Genome] maf files

[Emmanuel Buschiazzo]

Greetings,

I have a few questions regarding the multiz alignments found in maf files:

- Is there a straightforward way to find out the length of sequence 
aligned per species and per chromosome?
- Along the same lines, can I get the number of blocks per species and 
per chromosome?
- Lastly, how likely is it that blastz will split a repeat (transposable 
element, simple repeat..) between 2 adjacent blocks? In other words, can 
I assume that orthologous and rather short (<500bp) repeats will be 
preserved as entities in alignment blocks?

Thank you in general for your work, and in advance for your your help...

Emmanuel.

<mailto:ebr26 at student.canterbury.ac.nz>