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Plz give some info regarding DDBJ???

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Plz give some info regarding DDBJ???

Postby bioinfo » Thu Jan 27, 2011 12:11 pm

I want to retrive some nucleotide sequences from it.
I dont know about DAD.
In results hit they display many links
i want all nucleotide sequences of my gene .
I dont know i have to taken it from DDBJ or DAD or any other links.
Plz give some information..........fast......... :(
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Postby JackBean » Thu Jan 27, 2011 1:09 pm

by DDBJ you mean DNA Database of Japan, I guess. What do you mean by DAD?

If you're talking about BLAST search, you get only links to the sequence page.

Why don't you use PubMed insted? There you can have it in FASTA format,at least.

Plz give some explanation..........fast......... :(
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Postby bioinfo » Fri Jan 28, 2011 10:27 am

i want nucleotide sequences of gene trp5.
I think PubMed is used for literature search.
DAD & DDBJ are two different sequence libraries of DDBJ.
I dont know from where sequence should be taken.

-DAD has been produced by extracting alll translated sequences from the latest release of the INSDC.
- CON division entries are not included in current release of ARSA/DAD database.

i dont know about CON division.
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Postby canalon » Fri Jan 28, 2011 9:05 pm

Patrick

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Postby JackBean » Sat Jan 29, 2011 8:58 pm

PubMed has much more to offer than just a literature search. I think you should first have a look ;)
http://www.biolib.cz/en/main/

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Postby bioinfo » Mon Jan 31, 2011 9:05 am

I want sequences only from DDBJ.
means sequences which was submited through Japanies researchers.
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Postby JackBean » Mon Jan 31, 2011 4:24 pm

Why so? Do you think that Japanese are the best? :lol:

I think even into DDBJ can submit sequences non-Japanese researchers. You can always check, who submited the sequence.
http://www.biolib.cz/en/main/

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Postby bioinfo » Tue Feb 01, 2011 8:01 am

DDBJ contains most of the sequences from Japannese researchers not all. that i know.
I also know that DDBJ,EMBL & GenBank exchange their data by INSDC.
But i want to conferm this.
So i taken sequences from NCBI-GenBank,EMBL & now i want to take sequences from DDBJ.
But DDBJ gives only whole chromosome sequences & i want nucleotide sequences.
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Postby canalon » Tue Feb 01, 2011 10:17 pm

it seems that you should use that:
http://getentry.ddbj.nig.ac.jp/top-e.html
or
http://arsa.ddbj.nig.ac.jp/arsa/search/TopMenu

The first one seems basic and limited, the second page seems to offer more choice and waymore results for the same query (trp5).

Good luck
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Postby bioinfo » Wed Feb 02, 2011 11:02 am

I used
http://arsa.ddbj.nig.ac.jp/arsa/search/QuickSearch
You can see here that all sequences are of whole genome.
& i want only gene sequence.
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Postby canalon » Wed Feb 02, 2011 7:12 pm

Used that. Quick Search for trp5 in DDBJ (java script enabled in the database field) I have 212 hits (not all of trp5 at first glance with size starting at 110nt to indeed whole genomes. And the gene itself is the whole genome anyway, just look through the annotations.
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