NCBI Genbank and Reference Sequence

[rahbz]

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,

[GenoMax]

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/

[rahbz]

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.

[rhinoceros]

Install local db and use blastdbcmd? Or look into bioperl..