[Genome] Does MAF format for multiz17way with ref hg18 not have "i" or "e" lines?

Andrew Smith asmith at cshl.edu
Sat Feb 17 13:43:18 PST 2007


I've been using the multiz17way alignments, referenced on different species and 
assemblies. Today I thought I needed to use the "i" lines because I was 
manipulating the blocks in a way that would require looking to the adjacent 
blocks and merging them. In particular, I wanted to know if the sequence before 
or after a particular block is contiguous with the one in the block I'm 
examining, and your online help for MAF format says this is contained in the 
information line (starting with "i"). But I can't find these lines in hg18, hg17 
or mm8. I didn't look at every line of every file, but checked several 
chromosomes. When the sequences are contiguous, it is usually easy to spot 
because the end of one block is the start of the next (depending on strand). But 
this is not always the case, e.g., something may be either deleted, or aligned 
to another chromosome.

So are there still "i" lines in the MAF files? And if not, do you have any 
suggestions?

If from my question it seems like I don't understand these files, point me to 
more info please.

Thanks,
Andrew



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