[ensembl-dev] compara blastz coordinates

[Elena Grassi]

Thank you for your exaustive reply.

On Wed, Apr 11, 2012 at 12:56 PM, Javier Herrero <jherrero at ebi.ac.uk> wrote:
> The coordinates are given with respect to the end of the chromosome when the
> sequence is in the reverse strand.

If with "are given" you refer to the hypothetical output of the script
that I linked I've understood, while the data stored in the mysql
server and shown on the genome browser are always referring to the
start of the chromosome "a la entrez" if I've gotten this right.

For example:
hsapiens versus ggallus (compara57)

homo_sapiens:22 >  	chromosome:GRCh37:22:16114957:16115029:1
gallus_gallus:Z >  	chromosome:WASHUC2:Z:49606588:49606660:-1

homo_sapiens:22
GCCTGGTAGTAAAGTTGCCCTATTCCACTTCGTTTCTCTTCCTACATTTCTAAAGAGAAGAGACACAAATAAA
gallus_gallus:Z
GCTTGTCAGCAATATTCCTCTATTCAATCACATCTCGCTCTTTACATTTCTAAAAAGGCGAGATAAAAATAGA

Blatting the latter sequence against the ggallus genome brings me here:
   ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO
STRAND  START    END      SPAN
---------------------------------------------------------------------------------------------------
browser details YourSeq           73     1    73    73 100.0%     Z
-   49606588  49606660     73

Sorry for the confusion, I wasn't referring to the output of that
script (which as is does not run) but to the database data as is.

Thanks,
E.