[ensembl-dev] Eactracting Downstream Seq of Drosophila Melanogaster

Bukhari, Syed Abbas sbukhar at illinois.edu
Wed Apr 16 21:45:13 BST 2014


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:
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>   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
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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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