[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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