[ensembl-dev] Eactracting Downstream Seq of Drosophila Melanogaster
Rhoda Kinsella
rhoda at ebi.ac.uk
Thu Apr 17 09:14:20 BST 2014
Hi Syed,
Thank you for reporting this issue. We are currently looking into the cause of the problem. In the meantime, you can get the downstream sequences for Fly from the Ensembl Genomes BioMart databases here:
http://metazoa.ensembl.org/biomart/martview/
I hope that helps,
Regards
Rhoda
On 16 Apr 2014, at 21:45, "Bukhari, Syed Abbas" <sbukhar at illinois.edu> wrote:
> Hi I am trying to extract 2MB downstream sequence of a genes using biomart, but it is not allowing to do that on the ensembl biomart website. Is there any problem extracting downstream sequences for fly? Or should i consider extracting sequences using R?
>
> Thanks
> On Apr 16, 2014, at 10:07 AM, dev-request at ensembl.org wrote:
>
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>> Today's Topics:
>>
>> 1. Re: Gene and RS (Igo Medeiros)
>> 2. Re: Gene and RS (Igo Medeiros)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 16 Apr 2014 11:52:28 -0300
>> From: Igo Medeiros <igo701 at gmail.com>
>> Subject: Re: [ensembl-dev] Gene and RS
>> To: Ensembl developers list <dev at ensembl.org>
>> Message-ID:
>> <CAE5otB=oA=uC+9RT=a0P7NUqfSAD3BgXvAeCNyYxjhJyS1gmrA at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> I am study the documentation about VEP too.
>>
>>
>> 2014-04-16 11:52 GMT-03:00 Igo Medeiros <igo701 at gmail.com>:
>>
>>> How can I access gene table?
>>> I saw VEP, but i need study more about.
>>>
>>>
>>> 2014-04-16 11:16 GMT-03:00 Will McLaren <wm2 at ebi.ac.uk>:
>>>
>>> Have you considered using our Variant Effect Predictor tool (VEP)?
>>>>
>>>> http://www.ensembl.org/info/docs/tools/vep/index.html
>>>>
>>>> It's very useful for investigating novel variations found in sequencing
>>>> experiments and the like, and can probably give you a lot of the
>>>> information you need without having to write any code.
>>>>
>>>> The gene name is found in the xref (external reference) table, linked via
>>>> the display_xref_id column in the gene table:
>>>>
>>>> SELECT display_label
>>>> FROM gene g, xref x
>>>> WHERE g.display_xref_id = x.xref_id
>>>> AND g.stable_id = 'ENSG00000196218';
>>>>
>>>>
>>>> On 16 April 2014 14:55, Igo Medeiros <igo701 at gmail.com> wrote:
>>>>
>>>>> Thank you,
>>>>> both are help me.
>>>>> I was looking just in schema homo_sapiens_variation_75_37, not in
>>>>> homo_sapiens_core_75_37 too. Now I understand better why a lot of bases.
>>>>> I am usuing PHP ang JQuery, but I would like to change the project, that
>>>>> i am doing, to Perl and BioJS.
>>>>>
>>>>> There is a other thing. How can I find for gene name? I am looking for
>>>>> all schema, but until now not found.
>>>>>
>>>>> All this is because If don't exist the variation found in lab, in UFPA,
>>>>> in the schemas, I have to find all things connected with that area of
>>>>> sequence. And publications.
>>>>>
>>>>>
>>>>>
>>>>> 2014-04-16 10:02 GMT-03:00 Will McLaren <wm2 at ebi.ac.uk>:
>>>>>
>>>>> If you do want a quick way to get all rsIDs that fall in a gene, this
>>>>>> query should work:
>>>>>>
>>>>>> SELECT vf.variation_name
>>>>>> FROM homo_sapiens_variation_75_37.variation_feature vf,
>>>>>> homo_sapiens_core_75_37.gene g
>>>>>> WHERE g.seq_region_id = vf.seq_region_id
>>>>>> AND vf.seq_region_end >= g.seq_region_start
>>>>>> AND vf.seq_region_start <= g.seq_region_end
>>>>>> AND vf.source_id = 1
>>>>>> AND g.stable_id = 'ENSG00000196218'
>>>>>>
>>>>>> Replace ENSG00000196218 with the stable identifier of your gene of
>>>>>> interest. Remove "AND vf.source_id = 1" if you also want variation features
>>>>>> from sources that aren't dbSNP.
>>>>>>
>>>>>> As Kieron says, we would encourage you to use our perl API, REST API or
>>>>>> BioMart, all of which can accomplish this same task without the risks of
>>>>>> schema changes.
>>>>>>
>>>>>> The REST API is particularly suited to this sort of task; the following
>>>>>> URL retrieves all variants in a gene with ID ENSG00000157764:
>>>>>>
>>>>>>
>>>>>> http://beta.rest.ensembl.org/feature/id/ENSG00000157764?feature=variation;content-type=application/json
>>>>>>
>>>>>> See http://beta.rest.ensembl.org/documentation/info/feature_id for
>>>>>> more details.
>>>>>>
>>>>>> Regards
>>>>>>
>>>>>> Will McLaren
>>>>>> Ensembl Variation
>>>>>>
>>>>>>
>>>>>> On 16 April 2014 13:46, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:
>>>>>>
>>>>>>> Ensembl has a table for each genetic feature type, hence we have a
>>>>>>> Transcript table, a Gene table, and one for each class of variation. Each
>>>>>>> table shares a common set of fields, plus more that are specific to that
>>>>>>> feature. This is slightly contrary to a traditionally normalised schema.
>>>>>>>
>>>>>>> It is not clear to me what you mean by "RS inside a Gene". If you wish
>>>>>>> to understand our schema, please take a look at the following link.
>>>>>>>
>>>>>>> http://www.ensembl.org/info/docs/api/core/core_schema.html
>>>>>>>
>>>>>>> I urge you to find another way to access our data if at all possible.
>>>>>>> Direct SQL queries against our schema is sometimes the right solution, but
>>>>>>> suffers when we have to make changes in later releases. Our API and other
>>>>>>> services insulate you from these changes. Also, some commonly required data
>>>>>>> is computed and therefore cannot be found in the database at all.
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Kieron Taylor
>>>>>>> Ensembl Core
>>>>>>>
>>>>>>>
>>>>>>> On 16/04/2014 13:17, Igo Medeiros wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>> how can I found relation, in DB, between Gene and all RS inside Gene?
>>>>>>>> there are columns like seq_region_start, seq_region_end ans
>>>>>>>> seq_region_id those repeat in three tables(variation_feature,
>>>>>>>> structural_variation_feature and phenotype_feature), what the diferent
>>>>>>>> between them?
>>>>>>>> Sorry for my english, its not so good. And thank you for help.
>>>>>>>>
>>>>>>>> --
>>>>>>>> Igo Paix?o de Medeiros
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Dev mailing list Dev at ensembl.org
>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Igo Paix?o de Medeiros
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list Dev at ensembl.org
>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Dev mailing list Dev at ensembl.org
>>>> Posting guidelines and subscribe/unsubscribe info:
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>>>>
>>>>
>>>
>>>
>>> --
>>> Igo Paix?o de Medeiros
>>>
>>
>>
>>
>> --
>> Igo Paix?o de Medeiros
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Wed, 16 Apr 2014 12:07:28 -0300
>> From: Igo Medeiros <igo701 at gmail.com>
>> Subject: Re: [ensembl-dev] Gene and RS
>> To: Ensembl developers list <dev at ensembl.org>
>> Message-ID:
>> <CAE5otB=+zH1v9hjJ-n+anyvHnN87OYK91XSs43TV4q3hF+4XMw at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Sorry for my lack of attention. I saw the table.
>> Thank you for help.
>>
>>
>>
>> 2014-04-16 11:52 GMT-03:00 Igo Medeiros <igo701 at gmail.com>:
>>
>>> I am study the documentation about VEP too.
>>>
>>>
>>> 2014-04-16 11:52 GMT-03:00 Igo Medeiros <igo701 at gmail.com>:
>>>
>>> How can I access gene table?
>>>> I saw VEP, but i need study more about.
>>>>
>>>>
>>>> 2014-04-16 11:16 GMT-03:00 Will McLaren <wm2 at ebi.ac.uk>:
>>>>
>>>> Have you considered using our Variant Effect Predictor tool (VEP)?
>>>>>
>>>>> http://www.ensembl.org/info/docs/tools/vep/index.html
>>>>>
>>>>> It's very useful for investigating novel variations found in sequencing
>>>>> experiments and the like, and can probably give you a lot of the
>>>>> information you need without having to write any code.
>>>>>
>>>>> The gene name is found in the xref (external reference) table, linked
>>>>> via the display_xref_id column in the gene table:
>>>>>
>>>>> SELECT display_label
>>>>> FROM gene g, xref x
>>>>> WHERE g.display_xref_id = x.xref_id
>>>>> AND g.stable_id = 'ENSG00000196218';
>>>>>
>>>>>
>>>>> On 16 April 2014 14:55, Igo Medeiros <igo701 at gmail.com> wrote:
>>>>>
>>>>>> Thank you,
>>>>>> both are help me.
>>>>>> I was looking just in schema homo_sapiens_variation_75_37, not in
>>>>>> homo_sapiens_core_75_37 too. Now I understand better why a lot of bases.
>>>>>> I am usuing PHP ang JQuery, but I would like to change the project,
>>>>>> that i am doing, to Perl and BioJS.
>>>>>>
>>>>>> There is a other thing. How can I find for gene name? I am looking for
>>>>>> all schema, but until now not found.
>>>>>>
>>>>>> All this is because If don't exist the variation found in lab, in UFPA,
>>>>>> in the schemas, I have to find all things connected with that area of
>>>>>> sequence. And publications.
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2014-04-16 10:02 GMT-03:00 Will McLaren <wm2 at ebi.ac.uk>:
>>>>>>
>>>>>> If you do want a quick way to get all rsIDs that fall in a gene, this
>>>>>>> query should work:
>>>>>>>
>>>>>>> SELECT vf.variation_name
>>>>>>> FROM homo_sapiens_variation_75_37.variation_feature vf,
>>>>>>> homo_sapiens_core_75_37.gene g
>>>>>>> WHERE g.seq_region_id = vf.seq_region_id
>>>>>>> AND vf.seq_region_end >= g.seq_region_start
>>>>>>> AND vf.seq_region_start <= g.seq_region_end
>>>>>>> AND vf.source_id = 1
>>>>>>> AND g.stable_id = 'ENSG00000196218'
>>>>>>>
>>>>>>> Replace ENSG00000196218 with the stable identifier of your gene of
>>>>>>> interest. Remove "AND vf.source_id = 1" if you also want variation features
>>>>>>> from sources that aren't dbSNP.
>>>>>>>
>>>>>>> As Kieron says, we would encourage you to use our perl API, REST API
>>>>>>> or BioMart, all of which can accomplish this same task without the risks of
>>>>>>> schema changes.
>>>>>>>
>>>>>>> The REST API is particularly suited to this sort of task; the
>>>>>>> following URL retrieves all variants in a gene with ID ENSG00000157764:
>>>>>>>
>>>>>>>
>>>>>>> http://beta.rest.ensembl.org/feature/id/ENSG00000157764?feature=variation;content-type=application/json
>>>>>>>
>>>>>>> See http://beta.rest.ensembl.org/documentation/info/feature_id for
>>>>>>> more details.
>>>>>>>
>>>>>>> Regards
>>>>>>>
>>>>>>> Will McLaren
>>>>>>> Ensembl Variation
>>>>>>>
>>>>>>>
>>>>>>> On 16 April 2014 13:46, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:
>>>>>>>
>>>>>>>> Ensembl has a table for each genetic feature type, hence we have a
>>>>>>>> Transcript table, a Gene table, and one for each class of variation. Each
>>>>>>>> table shares a common set of fields, plus more that are specific to that
>>>>>>>> feature. This is slightly contrary to a traditionally normalised schema.
>>>>>>>>
>>>>>>>> It is not clear to me what you mean by "RS inside a Gene". If you
>>>>>>>> wish to understand our schema, please take a look at the following link.
>>>>>>>>
>>>>>>>> http://www.ensembl.org/info/docs/api/core/core_schema.html
>>>>>>>>
>>>>>>>> I urge you to find another way to access our data if at all possible.
>>>>>>>> Direct SQL queries against our schema is sometimes the right solution, but
>>>>>>>> suffers when we have to make changes in later releases. Our API and other
>>>>>>>> services insulate you from these changes. Also, some commonly required data
>>>>>>>> is computed and therefore cannot be found in the database at all.
>>>>>>>>
>>>>>>>> Regards,
>>>>>>>>
>>>>>>>> Kieron Taylor
>>>>>>>> Ensembl Core
>>>>>>>>
>>>>>>>>
>>>>>>>> On 16/04/2014 13:17, Igo Medeiros wrote:
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>> how can I found relation, in DB, between Gene and all RS inside Gene?
>>>>>>>>> there are columns like seq_region_start, seq_region_end ans
>>>>>>>>> seq_region_id those repeat in three tables(variation_feature,
>>>>>>>>> structural_variation_feature and phenotype_feature), what the
>>>>>>>>> diferent
>>>>>>>>> between them?
>>>>>>>>> Sorry for my english, its not so good. And thank you for help.
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Igo Paix?o de Medeiros
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Dev mailing list Dev at ensembl.org
>>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Igo Paix?o de Medeiros
>>>>>>
>>>>>> _______________________________________________
>>>>>> Dev mailing list Dev at ensembl.org
>>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list Dev at ensembl.org
>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Igo Paix?o de Medeiros
>>>>
>>>
>>>
>>>
>>> --
>>> Igo Paix?o de Medeiros
>>>
>>
>>
>>
>> --
>> Igo Paix?o de Medeiros
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>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>> End of Dev Digest, Vol 46, Issue 20
>> ***********************************
>
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> _______________________________________________
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> Ensembl Blog: http://www.ensembl.info/
Rhoda Kinsella Ph.D.
Ensembl Production Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton,
Cambridge
CB10 1SD
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