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Old 07-15-2013, 05:33 AM   #1
paraslonic
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Default download all available genomes by genus

Hi!
I`d like to get all bacterial genomes of some genus. There a lot of species already sequenced with a lot of strains as I can see in Genbank.
Is there a (semi)automatic way or maybe some soft to get all of them in fasta?
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Old 07-15-2013, 05:58 AM   #2
mastal
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Default download all available genomes by genus

You can download them by ftp from NCBI. See

http://www.ncbi.nlm.nih.gov/guide/data-software/

and click on the link FTP:Genome,

there should be a directory called Bacteria, with all the bacterial genomes.

You may also want to see the info on this page:

http://www.ncbi.nlm.nih.gov/guide/howto/dwn-genome/
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Old 07-16-2013, 01:08 AM   #3
paraslonic
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Thanks!
Though it seems not very convenient as some scripting will be needed to get all fastas and rename it to organism name
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Old 07-16-2013, 04:07 AM   #4
GenoMax
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You could just leave the Genbank ID in the file name intact and proceed with your analysis. You can always change the identifiers at the end of your analysis (depends on what you are looking to do).

wget/curl are handy unix utilities that can get you all the fasta files you need from the FTP link mastal posted above.
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Old 07-16-2013, 06:54 AM   #5
nickloman
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You might find these couple of shell commands helpful:
https://gist.github.com/nickloman/3974107
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Old 07-16-2013, 06:57 AM   #6
paraslonic
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2nickloman

Thanks!
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