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Old 06-21-2013, 09:37 AM   #1
rahbz
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Location: Kharagpur, India

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Default NCBI Genbank and Reference Sequence

Hi,

How can I download the complete fasta sequence from the Genbank ID or the NCBI reference sequence ID.
Download keeps on breaking while downloading, so I need to use wget on the FTP site with the given Genbank ID or reference ID
How could I get the ftp link from the ID.?
Thanks,
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Old 06-21-2013, 10:27 AM   #2
GenoMax
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Are you trying to download chromosome/genome size files or regular genbank files?

If you are looking for genomes then ftp from NCBI is located at

ftp://ftp.ncbi.nlm.nih.gov/

For regular Genbank ID's you could try the following (these sites would be closer to India)

http://www.ebi.ac.uk/ena/
http://www.ddbj.nig.ac.jp/


An additional option would be to use the NCBI e-utilities: http://www.ncbi.nlm.nih.gov/books/NBK25501/

Last edited by GenoMax; 06-21-2013 at 10:33 AM. Reason: Added info about e-utilities
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Old 06-21-2013, 08:13 PM   #3
rahbz
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Hi,
Thanks for the reply,
But even in those websites there is no direct link to the given accession number.
I need is FTP link to the given accession ID. Just like SRA which has the FTP link to each read that can be downloaded.
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Old 06-22-2013, 02:12 AM   #4
rhinoceros
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Install local db and use blastdbcmd? Or look into bioperl..

Last edited by rhinoceros; 06-22-2013 at 02:17 AM.
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