[ensembl-dev] compara blastz coordinates

[Stephen Fitzgerald]

Hi Elena,
the reference genome is always positive(1) but the non-reference 
can be positive or negative(-1):

For release 57, for example,
looking at the blastz alignments for
human (reference) vs chimp we get:

mysql> select gdb.name, ga.dnafrag_strand, count(*) from genomic_align ga 
inner join dnafrag df on df.dnafrag_id = ga.dnafrag_id inner join 
genome_db gdb on df.genome_db_id = gdb.genome_db_id  where 
ga.method_link_species_set_id = 388 group by gdb.name, ga.dnafrag_strand;
+-----------------+----------------+----------+
| name            | dnafrag_strand | count(*) |
+-----------------+----------------+----------+
| Homo sapiens    |              1 |   691239 |
| Pan troglodytes |             -1 |    82231 |
| Pan troglodytes |              1 |   609008 |
+-----------------+----------------+----------+

and for human (reference) vs mouse:
+--------------+----------------+----------+
| name         | dnafrag_strand | count(*) |
+--------------+----------------+----------+
| Homo sapiens |              1 |  1510836 |
| Mus musculus |             -1 |   712736 |
| Mus musculus |              1 |   798100 |
+--------------+----------------+----------+

Hope this helps,

Stephen.


On Mon, 26 Mar 2012, Elena Grassi wrote:

> Hello,
>
> I've looked around in the documentation but I'm not finding a straight
> answer so I'm posting here, I hope that this is not a very well hidden
> faq :)
>
> I'd like to download BlastZ-net/Lastz-net alignments from compara and
> store them in axt format. I'm using the APIs version 57 and from this
> source code:
> ftp://ftp.ensembl.org/pub/ensembl-compara/scripts/hcr/subsetAxtFromAndToCompara.pl
> and the UCSC documentations about axt:
> http://genome.ucsc.edu/goldenPath/help/axt.html
> I assumed that the non-reference species coordinates where given on
> the reverse complement strand when alignments fall on the negative
> strand but some manual tests via mysql seems to indicate that
> coordinates are always absolute (on the positive strand).
>
> Can someone help me?
> Thanks,
> Elena Grassi
> -- 
> http://www.mbcunito.it/
>
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