headers
Isaac cano | 1 Sep 2011 15:47
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Re: [BioMart Users] linkouturl for an attribute with no data

Dear Jack,


You are right, the problem was that columns contained the string 'NULL'. Thanks!

After solving this issue we are facing another issue. We have three data sources (ensembl, reactome and our local database). We have linked ensembl and reactome data sources by the ensembl gene id attribute and we have tried it's working. However, if in addition to the ensembl-reactome linkage we also link with our local database (linked with ensembl-reactome through the affy id) then we get no results for any query. We tried only linking our local database with ensembl and it worked. Does BioMart 0.8 RC6 support linking with more than one data source or the problem is with using ensembl gene id to link with reactome and affy id to link with our local database? Does the independentquerying Biomart property something to do?

Thanks!

Isaac

2011/8/26 Jack Hsu <Jack.Hsu <at> oicr.on.ca>
Hi Isaac,

BioMart displays "no data" when an empty string or NULL value is retrieved.

Can you check that the column value is NULL instead of the string 'NULL'?


Cheers,

-jack


From: Isaac cano <isaaccf <at> gmail.com>
Date: Fri, 26 Aug 2011 03:47:02 -0400
To: BioMart Users <users <at> biomart.org>
Subject: [BioMart Users] linkouturl for an attribute with no data

Dear BioMart users,

In our local database we store the PubMed IDs of experiments and we use the linkouturl property of the corresponding attribute in BioMart 0.8 rc6 to set a link for this attribute in the query results that links with the corresponding article in PubMed. It is the case that we have experiments with no PubMed IDs so in the query results we still get a link that if the attribute in the database is NULL by default the link is like NULL. 

I've seen that for example Ensembl present a "no data" value for those cases were actually there is no data but in this case the link is disabled. Is there a way to tell to BioMart not to create a link for attributes with no data ?

Thanks in advance,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona



--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: (+34)932 275 400, ext. 4182\4523
Mobile: (+34) 666 186 748
Fax: (+34) 932 275 455

_______________________________________________
Users mailing list
Users <at> biomart.org
https://lists.biomart.org/mailman/listinfo/users
Permalink | Reply | 6 comments |
headers
Arek Kasprzyk | 1 Sep 2011 16:00
Picon

Re: [BioMart Users] linkouturl for an attribute with no data

Hi Isaac,
to define the problem better ei to find out if this is data related or software related problem I suggest you do the following:

1. get ensembl <-> reactome set (through ensembl id)
2. get local <-> ensembl (through affy id)

then manually see if there is an intersection between those sets? If there is this is a software problem, if not it is a data problem

I hope i understood your linking correctly :)

a.




On Thu, Sep 1, 2011 at 9:47 AM, Isaac cano <isaaccf <at> gmail.com> wrote:
Dear Jack,

You are right, the problem was that columns contained the string 'NULL'. Thanks!

After solving this issue we are facing another issue. We have three data sources (ensembl, reactome and our local database). We have linked ensembl and reactome data sources by the ensembl gene id attribute and we have tried it's working. However, if in addition to the ensembl-reactome linkage we also link with our local database (linked with ensembl-reactome through the affy id) then we get no results for any query. We tried only linking our local database with ensembl and it worked. Does BioMart 0.8 RC6 support linking with more than one data source or the problem is with using ensembl gene id to link with reactome and affy id to link with our local database? Does the independentquerying Biomart property something to do?

Thanks!

Isaac

2011/8/26 Jack Hsu <Jack.Hsu <at> oicr.on.ca>
Hi Isaac,

BioMart displays "no data" when an empty string or NULL value is retrieved.

Can you check that the column value is NULL instead of the string 'NULL'?


Cheers,

-jack


From: Isaac cano <isaaccf <at> gmail.com>
Date: Fri, 26 Aug 2011 03:47:02 -0400
To: BioMart Users <users <at> biomart.org>
Subject: [BioMart Users] linkouturl for an attribute with no data

Dear BioMart users,

In our local database we store the PubMed IDs of experiments and we use the linkouturl property of the corresponding attribute in BioMart 0.8 rc6 to set a link for this attribute in the query results that links with the corresponding article in PubMed. It is the case that we have experiments with no PubMed IDs so in the query results we still get a link that if the attribute in the database is NULL by default the link is like NULL. 

I've seen that for example Ensembl present a "no data" value for those cases were actually there is no data but in this case the link is disabled. Is there a way to tell to BioMart not to create a link for attributes with no data ?

Thanks in advance,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona



--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona


_______________________________________________
Users mailing list
Users <at> biomart.org
https://lists.biomart.org/mailman/listinfo/users


_______________________________________________
Users mailing list
Users <at> biomart.org
https://lists.biomart.org/mailman/listinfo/users
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headers
Tesfaye Mersha | 1 Sep 2011 16:07

[BioMart Users] dbSNPs with functional category

Hi
 
I am looking SNP database which link SNPs with its functional classification like synonymous SNP, nonsynonymous SNP and other types.
 
I wish if you send me any Ensembl help resources as well as databases.
Thanks,
Tes
 
Tesfaye B. Mersha, Ph.D.
Assistant Professor
Cincinnati Children's Hospital Medical Center
Department of Pediatrics
University of Cincinnati
phone 513-803-2766
tesfaye.mersha <at> cchmc.org 
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Elena Rivkin | 1 Sep 2011 16:30
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Re: [BioMart Users] dbSNPs with functional category

Hi Tesfaye, 

In BioMart Martview (www.biomart.org/biomart/martview) you can query Ensembl variation data by selecting the following:

Database: Ensembl variaiton 63 
Dataset relevant to your species of interest (e.g. Homo sapiens Variation (dbSNP 132;ENSEMBL)

When you do that, you will see a selection of Filters and Attributes.  For example, under the GENE ASSOCIATED VARIATION FILTERS, you can select the Consequence type to include only synonymous SNPs, non-synonymous SNPS, and others (you can select multiple with the ctrl key)

Finally, select Attributes (eg. SNP ID, location, Ensembl Gene id, etc). 
Click on Results to view the data. 

Please let me know if you have other questions. 
 

Elena Rivkin, PhD
Outreach and Training Coordinator, Informatics and Bio-computing

Ontario Institute for Cancer Research
MaRS Centre, South Tower

101 College Street, Suite 800

Toronto, Ontario, Canada M5G 0A3


Tel: 647-258-4316

Toll-free: 1-866-678-6427

www.oicr.on.ca


This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

 


From: Tesfaye Mersha <Tesfaye.Mersha <at> cchmc.org>
Date: Thu, 1 Sep 2011 10:07:42 -0400
To: "users <at> biomart.org" <users <at> biomart.org>
Subject: [BioMart Users] dbSNPs with functional category

Hi
 
I am looking SNP database which link SNPs with its functional classification like synonymous SNP, nonsynonymous SNP and other types.
 
I wish if you send me any Ensembl help resources as well as databases.
Thanks,
Tes
 
Tesfaye B. Mersha, Ph.D.
Assistant Professor
Cincinnati Children's Hospital Medical Center
Department of Pediatrics
University of Cincinnati
phone 513-803-2766
tesfaye.mersha <at> cchmc.org 
_______________________________________________
Users mailing list
Users <at> biomart.org
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Isaac cano | 1 Sep 2011 16:42
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Re: [BioMart Users] linkouturl for an attribute with no data

Hi Arek,


I've checked that there is data intersection between ensembl, reactome and our local database like the following:

Ensembl Gene id       Affy_id              Pathway name
ENSG00000047249 221504_s_at Signaling by Insulin receptor
ENSG00000047249 221504_s_at Insulin receptor recycling
ENSG00000047249 221504_s_at HIV Infection
ENSG00000047249 221504_s_at Host Interactions of HIV factors
ENSG00000047249 221504_s_at Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters
ENSG00000047249 221504_s_at The role of Nef in HIV-1 replication and disease pathogenesis
ENSG00000047249 221504_s_at Nef Mediated CD4 Down-regulation
ENSG00000047249 221504_s_at Nef Mediated CD8 Down-regulation
ENSG00000047249 221504_s_at Transmembrane transport of small molecules
ENSG00000047249 221504_s_at Iron uptake and transport
ENSG00000047249 221504_s_at Transferrin endocytosis and recycling

The local database contains the affy_id, the ensembl gene id comes from ensembl and the pathway name comes from reactome. In this case, the problem should be a software problem I think. Any idea what should be going wrong?

Thanks for your help,

Isaac

2011/9/1 Arek Kasprzyk <arek.kasprzyk <at> gmail.com>
Hi Isaac,
to define the problem better ei to find out if this is data related or software related problem I suggest you do the following:

1. get ensembl <-> reactome set (through ensembl id)
2. get local <-> ensembl (through affy id)

then manually see if there is an intersection between those sets? If there is this is a software problem, if not it is a data problem

I hope i understood your linking correctly :)

a.




On Thu, Sep 1, 2011 at 9:47 AM, Isaac cano <isaaccf <at> gmail.com> wrote:
Dear Jack,

You are right, the problem was that columns contained the string 'NULL'. Thanks!

After solving this issue we are facing another issue. We have three data sources (ensembl, reactome and our local database). We have linked ensembl and reactome data sources by the ensembl gene id attribute and we have tried it's working. However, if in addition to the ensembl-reactome linkage we also link with our local database (linked with ensembl-reactome through the affy id) then we get no results for any query. We tried only linking our local database with ensembl and it worked. Does BioMart 0.8 RC6 support linking with more than one data source or the problem is with using ensembl gene id to link with reactome and affy id to link with our local database? Does the independentquerying Biomart property something to do?

Thanks!

Isaac

2011/8/26 Jack Hsu <Jack.Hsu <at> oicr.on.ca>
Hi Isaac,

BioMart displays "no data" when an empty string or NULL value is retrieved.

Can you check that the column value is NULL instead of the string 'NULL'?


Cheers,

-jack


From: Isaac cano <isaaccf <at> gmail.com>
Date: Fri, 26 Aug 2011 03:47:02 -0400
To: BioMart Users <users <at> biomart.org>
Subject: [BioMart Users] linkouturl for an attribute with no data

Dear BioMart users,

In our local database we store the PubMed IDs of experiments and we use the linkouturl property of the corresponding attribute in BioMart 0.8 rc6 to set a link for this attribute in the query results that links with the corresponding article in PubMed. It is the case that we have experiments with no PubMed IDs so in the query results we still get a link that if the attribute in the database is NULL by default the link is like NULL. 

I've seen that for example Ensembl present a "no data" value for those cases were actually there is no data but in this case the link is disabled. Is there a way to tell to BioMart not to create a link for attributes with no data ?

Thanks in advance,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona



--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona


_______________________________________________
Users mailing list
Users <at> biomart.org
https://lists.biomart.org/mailman/listinfo/users





--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: (+34)932 275 400, ext. 4182\4523
Mobile: (+34) 666 186 748
Fax: (+34) 932 275 455

_______________________________________________
Users mailing list
Users <at> biomart.org
https://lists.biomart.org/mailman/listinfo/users
Permalink | Reply | 4 comments |
headers
Arek Kasprzyk | 1 Sep 2011 16:47
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Re: [BioMart Users] linkouturl for an attribute with no data

In this case, it looks like a pointer problem.

Junjun: I believe Marie reported the same problem to you a few months ago. Marie do you want to shed some light on it?
Junjun: please confirm that this indeed the same problem and let us know if you made any progress on fxing that?

a

On Thu, Sep 1, 2011 at 10:42 AM, Isaac cano <isaaccf <at> gmail.com> wrote:
Hi Arek,

I've checked that there is data intersection between ensembl, reactome and our local database like the following:

Ensembl Gene id       Affy_id              Pathway name
ENSG00000047249 221504_s_at Signaling by Insulin receptor
ENSG00000047249 221504_s_at Insulin receptor recycling
ENSG00000047249 221504_s_at HIV Infection
ENSG00000047249 221504_s_at Host Interactions of HIV factors
ENSG00000047249 221504_s_at Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters
ENSG00000047249 221504_s_at The role of Nef in HIV-1 replication and disease pathogenesis
ENSG00000047249 221504_s_at Nef Mediated CD4 Down-regulation
ENSG00000047249 221504_s_at Nef Mediated CD8 Down-regulation
ENSG00000047249 221504_s_at Transmembrane transport of small molecules
ENSG00000047249 221504_s_at Iron uptake and transport
ENSG00000047249 221504_s_at Transferrin endocytosis and recycling

The local database contains the affy_id, the ensembl gene id comes from ensembl and the pathway name comes from reactome. In this case, the problem should be a software problem I think. Any idea what should be going wrong?

Thanks for your help,

Isaac

2011/9/1 Arek Kasprzyk <arek.kasprzyk <at> gmail.com>
Hi Isaac,
to define the problem better ei to find out if this is data related or software related problem I suggest you do the following:

1. get ensembl <-> reactome set (through ensembl id)
2. get local <-> ensembl (through affy id)

then manually see if there is an intersection between those sets? If there is this is a software problem, if not it is a data problem

I hope i understood your linking correctly :)

a.




On Thu, Sep 1, 2011 at 9:47 AM, Isaac cano <isaaccf <at> gmail.com> wrote:
Dear Jack,

You are right, the problem was that columns contained the string 'NULL'. Thanks!

After solving this issue we are facing another issue. We have three data sources (ensembl, reactome and our local database). We have linked ensembl and reactome data sources by the ensembl gene id attribute and we have tried it's working. However, if in addition to the ensembl-reactome linkage we also link with our local database (linked with ensembl-reactome through the affy id) then we get no results for any query. We tried only linking our local database with ensembl and it worked. Does BioMart 0.8 RC6 support linking with more than one data source or the problem is with using ensembl gene id to link with reactome and affy id to link with our local database? Does the independentquerying Biomart property something to do?

Thanks!

Isaac

2011/8/26 Jack Hsu <Jack.Hsu <at> oicr.on.ca>
Hi Isaac,

BioMart displays "no data" when an empty string or NULL value is retrieved.

Can you check that the column value is NULL instead of the string 'NULL'?


Cheers,

-jack


From: Isaac cano <isaaccf <at> gmail.com>
Date: Fri, 26 Aug 2011 03:47:02 -0400
To: BioMart Users <users <at> biomart.org>
Subject: [BioMart Users] linkouturl for an attribute with no data

Dear BioMart users,

In our local database we store the PubMed IDs of experiments and we use the linkouturl property of the corresponding attribute in BioMart 0.8 rc6 to set a link for this attribute in the query results that links with the corresponding article in PubMed. It is the case that we have experiments with no PubMed IDs so in the query results we still get a link that if the attribute in the database is NULL by default the link is like NULL. 

I've seen that for example Ensembl present a "no data" value for those cases were actually there is no data but in this case the link is disabled. Is there a way to tell to BioMart not to create a link for attributes with no data ?

Thanks in advance,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona



--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona


_______________________________________________
Users mailing list
Users <at> biomart.org
https://lists.biomart.org/mailman/listinfo/users





--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona


_______________________________________________
Users mailing list
Users <at> biomart.org
https://lists.biomart.org/mailman/listinfo/users
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headers
Isaac cano | 1 Sep 2011 16:58
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Re: [BioMart Users] linkouturl for an attribute with no data

Thanks Arek, Marie and Junjun for checking this problem! I hope there is a solution!


Thanks again!

Isaac

2011/9/1 Arek Kasprzyk <arek.kasprzyk <at> gmail.com>
In this case, it looks like a pointer problem.

Junjun: I believe Marie reported the same problem to you a few months ago. Marie do you want to shed some light on it?
Junjun: please confirm that this indeed the same problem and let us know if you made any progress on fxing that?

a


On Thu, Sep 1, 2011 at 10:42 AM, Isaac cano <isaaccf <at> gmail.com> wrote:
Hi Arek,

I've checked that there is data intersection between ensembl, reactome and our local database like the following:

Ensembl Gene id       Affy_id              Pathway name
ENSG00000047249 221504_s_at Signaling by Insulin receptor
ENSG00000047249 221504_s_at Insulin receptor recycling
ENSG00000047249 221504_s_at HIV Infection
ENSG00000047249 221504_s_at Host Interactions of HIV factors
ENSG00000047249 221504_s_at Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters
ENSG00000047249 221504_s_at The role of Nef in HIV-1 replication and disease pathogenesis
ENSG00000047249 221504_s_at Nef Mediated CD4 Down-regulation
ENSG00000047249 221504_s_at Nef Mediated CD8 Down-regulation
ENSG00000047249 221504_s_at Transmembrane transport of small molecules
ENSG00000047249 221504_s_at Iron uptake and transport
ENSG00000047249 221504_s_at Transferrin endocytosis and recycling

The local database contains the affy_id, the ensembl gene id comes from ensembl and the pathway name comes from reactome. In this case, the problem should be a software problem I think. Any idea what should be going wrong?

Thanks for your help,

Isaac

2011/9/1 Arek Kasprzyk <arek.kasprzyk <at> gmail.com>
Hi Isaac,
to define the problem better ei to find out if this is data related or software related problem I suggest you do the following:

1. get ensembl <-> reactome set (through ensembl id)
2. get local <-> ensembl (through affy id)

then manually see if there is an intersection between those sets? If there is this is a software problem, if not it is a data problem

I hope i understood your linking correctly :)

a.




On Thu, Sep 1, 2011 at 9:47 AM, Isaac cano <isaaccf <at> gmail.com> wrote:
Dear Jack,

You are right, the problem was that columns contained the string 'NULL'. Thanks!

After solving this issue we are facing another issue. We have three data sources (ensembl, reactome and our local database). We have linked ensembl and reactome data sources by the ensembl gene id attribute and we have tried it's working. However, if in addition to the ensembl-reactome linkage we also link with our local database (linked with ensembl-reactome through the affy id) then we get no results for any query. We tried only linking our local database with ensembl and it worked. Does BioMart 0.8 RC6 support linking with more than one data source or the problem is with using ensembl gene id to link with reactome and affy id to link with our local database? Does the independentquerying Biomart property something to do?

Thanks!

Isaac

2011/8/26 Jack Hsu <Jack.Hsu <at> oicr.on.ca>
Hi Isaac,

BioMart displays "no data" when an empty string or NULL value is retrieved.

Can you check that the column value is NULL instead of the string 'NULL'?


Cheers,

-jack


From: Isaac cano <isaaccf <at> gmail.com>
Date: Fri, 26 Aug 2011 03:47:02 -0400
To: BioMart Users <users <at> biomart.org>
Subject: [BioMart Users] linkouturl for an attribute with no data

Dear BioMart users,

In our local database we store the PubMed IDs of experiments and we use the linkouturl property of the corresponding attribute in BioMart 0.8 rc6 to set a link for this attribute in the query results that links with the corresponding article in PubMed. It is the case that we have experiments with no PubMed IDs so in the query results we still get a link that if the attribute in the database is NULL by default the link is like NULL. 

I've seen that for example Ensembl present a "no data" value for those cases were actually there is no data but in this case the link is disabled. Is there a way to tell to BioMart not to create a link for attributes with no data ?

Thanks in advance,

--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona



--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona


_______________________________________________
Users mailing list
Users <at> biomart.org
https://lists.biomart.org/mailman/listinfo/users





--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona





--
Isaac Cano
Bioinformatics
Linkcare Health Services SL
C/Villarroel 170
08036 - Barcelona
Tel.: (+34)932 275 400, ext. 4182\4523
Mobile: (+34) 666 186 748
Fax: (+34) 932 275 455

_______________________________________________
Users mailing list
Users <at> biomart.org
https://lists.biomart.org/mailman/listinfo/users
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headers
Parul Kudtarkar | 1 Sep 2011 20:13
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Favicon

[BioMart Users] retrieval of fasta sequence

Dear Biomart community,

Are there any biomart settings which would help me retrieve sequence data
and download in fasta format(i.e.
http://www.biomart.org/biomart/martview/58e633ee2248a0f3f179377de5a909d7).
Attached is a screen shot of how the sequence is currently displayed which
is not very convenient to view in browser.

Thanks and regards,
Parul Kudtarkar

--

-- 
Parul Kudtarkar
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org
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Elena Rivkin | 1 Sep 2011 21:19
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Re: [BioMart Users] retrieval of fasta sequence

Hi Parul, 

It seems that the sequence in your link is already in FASTA format
(below). 
>ENST00000008440|ENSG00000010072
MDDDLMLALRLQEEWNLQEAERDHAQESLSLVDASWELVDPTPDLQALFVQFNDQFFWGQ
LEAVEVKWSVRMTLCAGICSYEGKGGMCSIRLSEPLLKLRPRKDLVEVYHTFHDEVDEYR
RHWWRCNGPCQHRPPYYGYVKRATNREPSAHDYWWAEHQKTCGGTYIKIKEPENYSKKGK
GKAKLGKEPVLAAENKGTFVYILLIFM*
>ENST00000037502|ENSG00000034971
MRFFCARCCSFGPEMPAVQLLLLACLVWDVGARTAQLRKANDQSGRCQYTFSVASPNESS
CPEQSQAMSVIHNLQRDSSTQRLDLEATKARLSSLESLLHQLTLDQAARPQETQEGLQRE
LGTLRRERDQLETQTRELETAYSNLLRDKSVLEEEKKRLRQENENLARRLESSSQEVARL
RRGQCPQTRDTARAVPPGSREVSTWNLDTLAFQELKSELTEVPASRILKESPSGYLRSGE
GDTGCGELVWVGEPLTLRTAETITGKYGVWMRDPKPTYPYTQETTWRIDTVGTDVRQVFE
YDLISQFMQGYPSKVHILPRPLESTGAVVYSGSLYFQGAESRTVIRYELNTETVKAEKEI
PGAGYHGQFPYSWGGYTDIDLAVDEAGLWVIYSTDEAKGAIVLSKLNPENLELEQTWETN
IRKQSVANAFIICGTLYTVSSYTSADATVNFAYDTGTGISKTLTIPFKNRYKYSSMIDYN
PLEKKLFAWDNLNMVTYDIKLSKM*

Elena Rivkin, PhD
Outreach and Training Coordinator, Informatics and Bio-computing

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel: 647-258-4316
Toll-free: 1-866-678-6427
www.oicr.on.ca

This message and any attachments may contain confidential and/or
privileged information for the sole use of the intended recipient. Any
review or distribution by anyone other than the person for whom it was
originally intended is strictly prohibited. If you have received this
message in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this message may
not be that of the organization.

On 11-09-01 2:13 PM, "Parul Kudtarkar" <parulk <at> caltech.edu> wrote:

>Dear Biomart community,
>
>Are there any biomart settings which would help me retrieve sequence data
>and download in fasta format(i.e.
>http://www.biomart.org/biomart/martview/58e633ee2248a0f3f179377de5a909d7).
>Attached is a screen shot of how the sequence is currently displayed which
>is not very convenient to view in browser.
>
>Thanks and regards,
>Parul Kudtarkar
>
>-- 
>Parul Kudtarkar
>Scientific Programmer
>Center for Computational Regulatory Genomics
>Beckman Institute,
>California Institute of Technology
>http://www.spbase.org

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headers
Junjun Zhang | 1 Sep 2011 21:32
Picon

Re: [BioMart Users] retrieval of fasta sequence

I guess Parul tries to achieve that in his BioMart 0.8 server.

At this time, it is not supported if the sequence result is produced by a
normal data query, ie, sequence is kept in database using a varchar
column. We will consider supporting this in future releases.

We do have a specialized tool that provides access to various of sequences
(http://central.biomart.org/sequence/?gui=Sequence_retrieval&mart=metaseq_m
art_63_config). However, this is not current officially supported and is
not recommended for external use.

Kind regards,

Junjun

On 11-09-01 3:19 PM, "Elena Rivkin" <Elena.Rivkin <at> oicr.on.ca> wrote:

>Hi Parul, 
>
>It seems that the sequence in your link is already in FASTA format
>(below). 
>>ENST00000008440|ENSG00000010072
>MDDDLMLALRLQEEWNLQEAERDHAQESLSLVDASWELVDPTPDLQALFVQFNDQFFWGQ
>LEAVEVKWSVRMTLCAGICSYEGKGGMCSIRLSEPLLKLRPRKDLVEVYHTFHDEVDEYR
>RHWWRCNGPCQHRPPYYGYVKRATNREPSAHDYWWAEHQKTCGGTYIKIKEPENYSKKGK
>GKAKLGKEPVLAAENKGTFVYILLIFM*
>>ENST00000037502|ENSG00000034971
>MRFFCARCCSFGPEMPAVQLLLLACLVWDVGARTAQLRKANDQSGRCQYTFSVASPNESS
>CPEQSQAMSVIHNLQRDSSTQRLDLEATKARLSSLESLLHQLTLDQAARPQETQEGLQRE
>LGTLRRERDQLETQTRELETAYSNLLRDKSVLEEEKKRLRQENENLARRLESSSQEVARL
>RRGQCPQTRDTARAVPPGSREVSTWNLDTLAFQELKSELTEVPASRILKESPSGYLRSGE
>GDTGCGELVWVGEPLTLRTAETITGKYGVWMRDPKPTYPYTQETTWRIDTVGTDVRQVFE
>YDLISQFMQGYPSKVHILPRPLESTGAVVYSGSLYFQGAESRTVIRYELNTETVKAEKEI
>PGAGYHGQFPYSWGGYTDIDLAVDEAGLWVIYSTDEAKGAIVLSKLNPENLELEQTWETN
>IRKQSVANAFIICGTLYTVSSYTSADATVNFAYDTGTGISKTLTIPFKNRYKYSSMIDYN
>PLEKKLFAWDNLNMVTYDIKLSKM*
>
>
>
>Elena Rivkin, PhD
>Outreach and Training Coordinator, Informatics and Bio-computing
>
>Ontario Institute for Cancer Research
>MaRS Centre, South Tower
>101 College Street, Suite 800
>Toronto, Ontario, Canada M5G 0A3
>
>Tel: 647-258-4316
>Toll-free: 1-866-678-6427
>www.oicr.on.ca
>
>This message and any attachments may contain confidential and/or
>privileged information for the sole use of the intended recipient. Any
>review or distribution by anyone other than the person for whom it was
>originally intended is strictly prohibited. If you have received this
>message in error, please contact the sender and delete all copies.
>Opinions, conclusions or other information contained in this message may
>not be that of the organization.
> 
>
>
>
>
>
>On 11-09-01 2:13 PM, "Parul Kudtarkar" <parulk <at> caltech.edu> wrote:
>
>>Dear Biomart community,
>>
>>Are there any biomart settings which would help me retrieve sequence data
>>and download in fasta format(i.e.
>>http://www.biomart.org/biomart/martview/58e633ee2248a0f3f179377de5a909d7)
>>.
>>Attached is a screen shot of how the sequence is currently displayed
>>which
>>is not very convenient to view in browser.
>>
>>Thanks and regards,
>>Parul Kudtarkar
>>
>>-- 
>>Parul Kudtarkar
>>Scientific Programmer
>>Center for Computational Regulatory Genomics
>>Beckman Institute,
>>California Institute of Technology
>>http://www.spbase.org
>
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