[Genome] pairwise alignments hg18/mm9 axt files

[Brooke Rhead]

Hello Daniel,

I assume you are looking at the file chr8_random.mm9.hg18.net.axt.gz, 
which contains human sequence aligned to mouse sequence, and not 
chr8_random.hg18.mm9.net.axt.gz, which contains mouse sequence aligned 
to human sequence.

There is a description of axt files here: 
http://genome.ucsc.edu/goldenPath/help/axt.html .

In the file chr8_random.mm9.hg18.net.axt.gz, the first line of sequence 
in each alignment is from mouse (the primary organism), and the second 
line of sequence is human (the aligning organism).  Every mouse sequence 
in this file is from chr8_random, and the human sequences come from 
various chromosomes (chr22 in this file is referring to human).

Regarding your question about alignment 186, note that (from the 
description page linked above):

If the strand value is "-", the values of the aligning organism's start 
and end fields are relative to the reverse-complemented coordinates of 
its chromosome.

So, the first line of sequence in alignment 186 is from mm8 
chr8_random:368,165-368,486.  The second line of sequence is from hg18 
chr8:6,882,742-6,883,068.

You can use the following formula to convert minus-strand axt 
coordinates to Genome Browser display coordinates:

         start = (chromSize - axtEnd) + 1
        	end = chromSize - (axtStart - 1)

In this case, the size of human chr8 is 146,274,826, so:

start = 146274826 - 139392085 + 1 = 6882742
end = 146274826 - (139391759 - 1) = 6883067

I hope this explanation helps.  If you have further questions, please 
feel free to contact us again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



danielh at mrc-lmb.cam.ac.uk wrote:
> Hi,
> 
> I have downloaded the axt files for the human/mouse pairwise alignments
> hg18/mm9. In the file for chr8_random, in alignment 186, the alignment
> start for the mouse chromosome is 139,391,759 while the size of the whole
> mouse chromosome (chr8) is 131,738,871. How can this be? In addition, the
> alignment 193 is aligned to mouse chromosome 22 although there is no mouse
> chromosome 22. There seem to be more strange entries like these in some of
> the "random" files. Is there an explanation for that?
> 
> thanks,
> Daniel
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome