[ensembl-dev] Our treatment of pseudoautosomal regions (PAR)

[Giulietta]

Dear all,

Ensembl is reviewing how we provide access to pseudoautosomal regions 
(PAR) in human, and we'd like your input.

Please let us know how our current PAR strategy works for you. What do 
you like and what is difficult? If our current strategy (explained 
below) is not working for you, please let us know why. (If it does work 
for you, we'd also like to know why!)

The pseudoautosomal regions (PAR), where chromosome X and Y share 
homologous sequence, are defined by the GRC for human. In Ensembl, the 
full-length Y chromosome is displayed on our browser. However, within 
our core human database, the Y chromosome is divided into five regions:

chromosome:GRCh38:Y:1:10000:1 unique to Y
chromosome:GRCh38:Y:10001:2781479:1 PAR1
chromosome:GRCh38:Y:2781480:56887902:1 unique to Y
chromosome:GRCh38:Y:56887903:57217415:1 PAR2
chromosome:GRCh38:Y:57217416:57227415:1 unique to Y

We store sequence for only the three unique regions of Y in our 
database. The DNA for PAR1 and PAR2 are stored with the sequence for 
chromosome X. The full-length chromosome Y can be generated on-the-fly 
by our API, where we stitch in the shared PAR sequence from X.

What does this mean practically?

- chr Y PARs are identical (ie. same set of contigs in the same order) 
for human X and Y. When aligning data such as RNA-seq to the genome, 
masking out the PAR on Y avoids duplicate mappings. This impacts mapping 
scores.

- Genes are only built on the X PAR regions only. (The genes you see in 
the Y PAR regions are identical to the genes annotated on X.)

Accessing PARs on the Y chromosome:

- Our Perl API provides a range of methods that allow you to fetch only 
the unique regions of Y or the whole of Y

- Our websites (e.g. www.ensembl.org) show genomic sequence for chr Y PAR

- Our FTP site provides a fasta file for the whole length of Y, with 
PARs replaced with Ns

Do feedback any comments by responding to this post, or let us know what 
you think on helpdesk (at) ensembl.org

Best wishes,
Giulietta (Ensembl Outreach)

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