<div dir="ltr"><div><div>Through the Perl API you can retrieve a GenomeBlock for Human-Tarsier LASTZ_NET alignment.  This can be seen in the website.<br><br><a href="http://uswest.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=699--Tarsius_syrichta--GeneScaffold_12:55117-149885;db=core;g=ENSG00000003096;r=X:117972731-117972828" target="_blank">http://uswest.ensembl.org/<wbr>Homo_sapiens/Location/Compara_<wbr>Alignments?align=699--Tarsius_<wbr>syrichta--GeneScaffold_12:<wbr>55117-149885;db=core;g=<wbr>ENSG00000003096;r=X:117972731-<wbr>117972828</a><br><br></div>I have also confirmed it locally using the latest perl API.<br><br></div>However, the same query via the REST API only returns the human sequence.<br><div><div><div><div><br><a href="http://rest.ensembl.org/alignment/region/homo_sapiens/X:117972731-117972828:-1/?content-type=application/json;method=LASTZ_NET;species_set=homo_sapiens;species_set=tarsius_syrichta" target="_blank">http://rest.ensembl.org/<wbr>alignment/region/homo_sapiens/<wbr>X:117972731-117972828:-1/?<wbr>content-type=application/json;<wbr>method=LASTZ_NET;species_set=<wbr>homo_sapiens;species_set=<wbr>tarsius_syrichta</a><br><br></div><div>Human-Gorilla is also affected.  What is special about Human-Tarsier and Human-Gorilla is that both are missing branch-length information in the database.  Looking through the REST API code, I believe the problem is occurring when the GenomeAlignBlock is being converted to a GenomicAlignTree here: <br><br><a href="https://github.com/Ensembl/ensembl-rest/blob/release/87/lib/EnsEMBL/REST/Model/GenomicAlignment.pm#L113-L125">https://github.com/Ensembl/ensembl-rest/blob/release/87/lib/EnsEMBL/REST/Model/GenomicAlignment.pm#L113-L125</a><br><br></div><div>When I call fetch_all_by_MethodLinkSpeciesSet_Slice using the perl API, locally, I can see both sequences, so I'm assuming that they are being dropped afterwards.<br></div><div><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>--<br>Reed A. Cartwright, PhD<br>Barrett Honors Faculty<br>Assistant Professor of Genomics, Evolution, and Bioinformatics<br>School of Life Sciences<br>Human and Comparative Genomics Laboratory<br>The Biodesign Institute<br>Arizona State University<br>==================<br>Availability: <a href="http://links.asu.edu/CartwrightCalendar" target="_blank">http://links.asu.edu/CartwrightCalendar</a><br>Address: The Biodesign Institute, PO Box 875301, Tempe, AZ 85287-5301 USA<br>Packages: The Biodesign Institute, 1001 S. McAllister Ave, Tempe, AZ 85287-5301 USA<br>Office: Biodesign B-220C, 1-480-965-9949<br>Website: <a href="http://cartwrig.ht/" target="_blank">http://cartwrig.ht/</a></div></div></div></div></div></div></div></div></div></div>
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