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Old 11-05-2012, 03:03 AM   #1
thedamian
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Default Download RefSeq .gb files based on accession number

Hi,
I have a list of genomic accession numbers (e.g. NG_007941.2, NG_009018.1).
I'd like to download .gb files based on these identifiers.

Manually, I can type it in NCBI and I got the page, e.g.
http://www.ncbi.nlm.nih.gov/nuccore/...report=genbank

then I click: "send", Choose Destination "File", Format: GenBank "CreateFile".

Is there any automatic way to obtain such files?

I've tried BioPerl and Bio:B::EUtilities, but I don't see any clear way how to do this.
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Old 11-05-2012, 03:45 AM   #2
GenoMax
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You can use the Entrez e-utilities. See this page and choose your preferred method.

https://www.ncbi.nlm.nih.gov/guide/howto/dwn-records/
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Old 11-06-2012, 04:48 AM   #3
thedamian
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Quote:
Originally Posted by GenoMax View Post
You can use the Entrez e-utilities. See this page and choose your preferred method.

https://www.ncbi.nlm.nih.gov/guide/howto/dwn-records/
Thank you very much!
I've found this http://www.ncbi.nlm.nih.gov/books/NB...trieving_large
after little modifications, it does exactly what I need!
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Old 12-13-2012, 12:25 AM   #4
thedamian
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@GenoMax, do you know if there is any robust way to download sequences of pseudogenes of the gene?

I have already GBK RefSeqGene sequences and additionaly I'd like to have corresponding pseudogenes sequences, for example:
NF1.gbk - GBK validated by RefSeqGene, downloaded based on accession number
NF1_p1.gbk - pseudogene 1
NF1_p2.gbk - pseudogene 2
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Old 12-13-2012, 04:31 AM   #5
GenoMax
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Quote:
Originally Posted by thedamian View Post
@GenoMax, do you know if there is any robust way to download sequences of pseudogenes of the gene?

I have already GBK RefSeqGene sequences and additionaly I'd like to have corresponding pseudogenes sequences, for example:
NF1.gbk - GBK validated by RefSeqGene, downloaded based on accession number
NF1_p1.gbk - pseudogene 1
NF1_p2.gbk - pseudogene 2
How about adding "pseudo" or "pseudogene" to your search terms. e.g. NF1 AND Pseudogene (note: AND has to be in capital).
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