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Limiting number of NCBI search results and downloading sequences

My goal is to download a specific number of sequences (eg. 1 million) from the NCBI protein database but exclude a specific organism. I can do an Entrez search to exclude the organism, but I can't find a way to limit the number of sequences I download. It's also not feasible to download all results (too large for the NCBI website).

Is there a particular Entrez command or script that would allow this? There was a similar question posted previously, but no direct answer was found.

Also, is there a more effective way to download sequences from search results other than selecting the 'Send to: file' drop down menu in the upper right of the screen? Often, when downloading larger numbers of sequences the connection ultimately breaks.

Thanks for your help! Please direct me/correct me if this question has in fact been already answered.

ncbi search
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written by jmah • jmah

1 answer

You could download the fasta file for nr sequence database here. Limiting your search to a million would need to be done carefully since you may bias your dataset for certain organisms (I am not sure what order NCBI puts those sequences in the file). I would use this solution afterwards: A: Choosing Random Set Of Seqs From Larger Set

You could exclude the species you don't want after sampling or you could remove them from original nr file with a solution like this (there are more on biostars): How To Remove Certain Sequences From A Fasta File

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written by GenoMax GenoMax

Thank you very much! Exactly what I was looking for. Also, thanks for the heads up about bias.

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written by jmah • jmah

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