[BioMart Users] retrieval of fasta sequence

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[BioMart Users] retrieval of fasta sequence

Parul Kudtarkar
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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Re: [BioMart Users] retrieval of fasta sequence

Elena Rivkin
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" <[hidden email]> 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

_______________________________________________
Users mailing list
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Re: [BioMart Users] retrieval of fasta sequence

Junjun Zhang
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" <[hidden email]> 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" <[hidden email]> 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
>
>_______________________________________________
>Users mailing list
>[hidden email]
>https://lists.biomart.org/mailman/listinfo/users

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users