Question: convert gisaid Accession number to genbank id
0
gravatar for janghj12000
3.0 years ago by
janghj120000 wrote:

Hello

I have a list of gisaid's HA accession numbers. (such as EPI539474, EPI416411)

Looking up wikipedia, the definition of "accession number" is "unique identifier given to a DNA or protein sequence record to allow for tracking of different versions of that sequence record and the associated sequence over time in a single data repository."

I would like to convert these accession numbers to genbank id.

Do you think it is possible?

If it is, can you tell me how I do that ?

Thank you

ADD COMMENTlink modified 3.0 years ago by natasha.sernova3.4k • written 3.0 years ago by janghj120000

Those are influenza strains?

ADD REPLYlink written 3.0 years ago by genomax64k

Yes it is. As I mentioned it is from gisaid

ADD REPLYlink written 3.0 years ago by janghj120000

I've asked NCBI about numbers you provided, it didn't recognize anything like that.

Below there are other web- sites with some information.

https://en.wikipedia.org/wiki/GISAID - some introdution

http://omictools.com/gisaid-epiflu-database-tool - in the right upper corner press 'I agree', and after that 'Join community'

After that you will submit some information about you, and hopefully, you will have access to their database

There are a lot of other information about GISAID, like file below

http://ecdc.europa.eu/en/press/events/Documents/ECDC-WHO-influenza-meeting-Daniels.pdf

I would suggest - try blastn with your sequences at NCBI, hopefully it will help to find the respective accession

numbers of nucleotide sequences you have. They provide even batch-method if you have a lot of them.

NCBI-web site is below:

www.ncbi.nlm.nih.gov

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by natasha.sernova3.4k

It appears that this information may only be available from the GSAID platform database (which requires registration).

ADD REPLYlink written 3.0 years ago by genomax64k

Unfortunately this looks possible. I could not register here. http://omictools.com/gisaid-epiflu-database-tool And the isolates are not reachable. That's very sad. Many thanks! Natasha

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by natasha.sernova3.4k
0
gravatar for natasha.sernova
3.0 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

It turned out there is a flu-database at NCBI.

http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html

Hopefully it will help you.

I just looked inside the paper below.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4527594/

But gisaid-database is not reachable without permission.

I hope it may be a probable solution to your problem.

Please, look at this paper below and at the table inside:

http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=21366

You will find many if not all known flu-epedemy HAs there.

As well as the viruses where they are from. I've already seen some of them

in NCBI FLU-database, so you have a chance.

Good luck!

It was so interesting to me that I've started the work for you.

I've searched for HA in NCBI FLU-database.

http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi?go=database

I found about 6000 partial sequences of HA like this one below.

And occasionally I found the following url: ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/

Look at it. It seems useful. To my mind it contains currently known flu genomic information from NCBI.

Below is an example of my search in the FLU-database in NCBI.

  • I've found a fragment of HA in aminoacids from some Influenza A virus with different ids. etc.

hemagglutinin, partial [Influenza A virus (A/Afghanistan/AF1168/2008(H3N2))]

GenBank: ACD13250.1

GenPept Identical Proteins Graphics

gi|187606959|gb|ACD13250.1| hemagglutinin, partial [Influenza A virus (A/Afghanistan/AF1168/2008(H3N2))] QKFPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQSSSTGEICDSPHQILDGENCTLIDAL LGDPQCDGFQNKNWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACI RRSNNSFFSRLNWLTHSKFKYPALNVTMPNNENFDKLYIWGVHHPGTDNDQIFLYAQASGRITVSTKRSQ QTVIPNIGSRPRVRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSK CITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMV

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by natasha.sernova3.4k
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