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Brassica Information Portal
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Sequence Identifiers to SeqStore? #478

Open teatree1212 opened 8 years ago

teatree1212 commented 8 years ago

I am trying to make out what the numbers ( marked in red) are. I suspect that they are Sequence identifiers which refer to the SeqStore. The corresponding sequence ( or a link to it to a table hosting it) should occur instead of the identifier:

screen shot 2016-04-18 at 17 19 30
Nuanda commented 8 years ago

Do you mean that one: http://www.interstoredb.org/Brassica/ss/seqstore.html ?

teatree1212 commented 8 years ago

this website is currently unavailable. but I do mean SeqStore, as it is the repository for all the marker and ESTs..

Nuanda commented 8 years ago

Are you in contact with the maintainers of this website?

teatree1212 commented 8 years ago

I made out someone who has an old dump and will receive the data from there.

Nuanda commented 8 years ago

I might have a dump of that (it's called als_dbdump_CORE... - not sure if this is what is needed) from 2014-06-16 - in case you can't get anything newer (should be in sync with the CS data we have).

It's an SQL dump. Could you tell me what tables should I look for? I.e. where to look for the sequences denoted with the 4-digit identifier in the screenshot you posted?

Nuanda commented 8 years ago

@teatree1212 With the '9. Sequence store' item in the Word document I meant this issue. Are there any plans regarding this?

teatree1212 commented 8 years ago

I have the sequences and their associated identifiers for this. So would you create a 'sequence' table for them? They are not part of any external sequence storage facility ( except SeqStore, which is down at the moment)

Ultimately, these marker sequences are to be aligned with the genome of the respective brassica sequence, so that they can be visualised in the EnsemblePlants genome Browser. Then we could cross-link them to these locations.

Nuanda commented 8 years ago

I guess showing that through an external, dedicated viewer like Ensembl is preferable. BIP has no special facility to adequately show sequences, other than let a user download them.

wjurkowski commented 8 years ago

Could we visualise them through TGAC browser?

2016-07-19 12:36 GMT+01:00 Tomasz Gubała notifications@github.com:

I guess showing that through an external, dedicated viewer like the Ensembl is preferable. BIP has no special facility to adequately show sequences, other than let the users download them.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/TGAC/brassica/issues/478#issuecomment-233606276, or mute the thread https://github.com/notifications/unsubscribe-auth/ADVH8Gode_Bj8vuXzvtEknG9-z7UCAYWks5qXLa2gaJpZM4IJ4rP .

teatree1212 commented 8 years ago

I sent these sequences away to Ensembl for a BLAST against their reference genome. Once that is done- checked- and confirmed, we can cross-link to those locations. I think that it might even be a good idea to use the TGAC browser. I will ask Anil about this. it might be a bit of work, so I don't know how much time he can allocate to this.

Nuanda commented 8 years ago

@teatree1212 We were discussing linking from TGAC browser to BIP, and Anil did that, as I understand. But chances are here you mean the other way around, linking from BIP tables to the TGAC Browser, right?

wjurkowski commented 8 years ago

Yes, please

2016-09-28 13:38 GMT+01:00 Tomasz Gubała notifications@github.com:

@teatree1212 https://github.com/teatree1212 We were discussing linking from TGAC browser to BIP, and Anil did that, as I understand. But chances are here you mean the other way around, linking from BIP tables to the TGAC Browser, right?

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