[ensembl-dev] ensembl genomes 18_71 protein sequences not returned properly

Moretti Sébastien sebastien.moretti at unil.ch
Tue Apr 30 09:21:49 BST 2013


Hi James

looks good now.
Thanks

> Hello,
> Thanks for bringing this to our attention; the all-N sequences were due to some missing data in one of the databases on the public mysql server. This has been rectified, and the queries should now work.
>
> Thanks,
> James
>
>
> On Mon, 29 Apr 2013 14:11:50 +0200
> Moretti Sébastien <sebastien.moretti at unil.ch> wrote:
>
>> Hi
>>
>> I would like to extract protein and nucleotide CDS related sequences
>> from Drosophila ensembl gene trees with API 71 on ensembl metazoa 18.
>>
>> I get some warnings (see at the bottom of the e-mail) for each tree and
>> get nucleotide sequences that look fine. But all protein sequences look
>> the same, all amino acid letters are N.
>> e.g.
>>   >FBpp0227954
>> ----------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------NNNN
>> NNNNNNNNN----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>
>>
>>   From a tree object, I use $tree->get_SimpleAlign to get the protein
>> MSA, and $tree->get_SimpleAlign(-cdna=>1) for the nucleotide CDS MSA.
>>
>>
>> I used the same script last week on Glires taxon on ensembl 71 and
>> everything looked fine.
>>
>>
>> Has something changed in the API ?
>>
>>
>> Use of uninitialized value $sequence in substr at
>>
>> /usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMember.pm
>> line 467 (#1)
>> substr outside of string at
>>
>> /usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMember.pm
>> line 467 (#2)
>> Use of uninitialized value $substring in pattern match (m//) at
>>
>> /usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMember.pm
>> line 468 (#1)
>> Use of uninitialized value in numeric lt (<) at
>>
>> /usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMember.pm
>> line 473 (#1)
>> Use of uninitialized value in subtraction (-) at
>>
>> /usr/local/ensembl/ensembl-compara/modules//Bio/EnsEMBL/Compara/AlignedMember.pm
>> line 474 (#1)
>>
>>
>> Regards

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/




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