[ensembl-dev] How to retrieve the ancestral sequences via compara perl API?

Tang, Haiming ningzhithm at gmail.com
Fri Sep 26 18:31:04 BST 2014


Dear group,

I want to retrieve the ancestral sequences via compara API.

So I used

my $mlss = $mlss_adaptor->fetch_by_method_link_type_species_set_name("EPO",
"mammals");

my $slice = $slice_adaptor->fetch_by_region('toplevel', $seq_region,
$seq_region_start, $seq_region_end);

my $genomic_align_blocks =$genomic_align_block_adaptor
->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss,  $slice);


(I also attached my script  below.)

But instead of ancestral sequences, I get multiple alignments of the
current species.

which look like:

homo_sapiens/11/34888581-35077850
------------------------------------------------------------

felis_catus/D1/90701788-90852536
gggaacagaacacagcatgagaccatgctcagaacagatttcattcaggggctataa-aa

canis_familiaris/18/32879322-33028613
aggaacagaatatagcatgatcacatactca-------attcattcagtggctatattaa

equus_caballus/12/1619359-1776531
aggaacagggtggtg--cgacccct---------------tcctggaggggacc--tc--

sus_scrofa/2/28305627-28477519
gggaaccgaacatggcatgattac----gtgatactgattctattcaggggctatattaa

ovis_aries/15/63610201-63792541
gggaacagaacatagcatgattattcactgtgtactgatttcattcaggggctatactaa

bos_taurus/15/66212217-66395858
gggaacagaacacagcacaattattccctgtatactgatttcattcaggggctatactaa

rattus_norvegicus/3/99477347-99634398
------------------------------------------------------------

mus_musculus/2/102948690-103088848
------------------------------------------------------------

oryctolagus_cuniculus/1/174190771-174392712
------------------------------------------------------------

macaca_mulatta/14/36757737-36941679
------------------------------------------------------------

papio_anubis/14/29787300-29976716
------------------------------------------------------------

gorilla_gorilla/11/35459310-35656044
------------------------------------------------------------

pan_troglodytes/11/34873765-35067421
------------------------------------------------------------

pongo_abelii/11/34236125-34418629
------------------------------------------------------------

callithrix_jacchus/11/98105861-98306401
------------------------------------------------------------

But according to "
http://uswest.ensembl.org/info/genome/compara/analyses.html#ancestral"

" Each ancestral sequence is named according to the derived extant species.
For example, a sequence named Hsap, Ptro, Mmul corresponds to the ancestor
of the *Homo sapiens*, *Pan troglodytes*, and*Macaca mulatta* genomes."

Why am I not getting ancestral sequences? And how can I get ancestral
sequences?

Thank you in advance.

Haiming
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