Where to find 'nr. Non-redundant GenBank...' the peptide sequence database?
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6 months ago
matt ▴ 20

Were can find a download page of the 'nr. Non-redundant GenBank CDS translations + PDB + SwissProt + PIR + PRF, excluding those in env_nr.' in FASTA format as used e.g. for BLAST-ing on NCBI website, https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome?

database genbank • 267 views
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6 months ago
GenoMax 108k

You can find pre-made nr indexes on NCBI's site (LINK). You will need to download ALL nr* files (44 pieces as of today).

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Thanks GenoMax, but how do I paste it together to use with local BLAST? Usually, after downloading e.g. UniProt, I would jus do

makeblastdb.exe -in .\uniprot-reviewed_yes_5species.fasta -dbtype prot

following (https://angus.readthedocs.io/en/2019/running-command-line-blast.html). Btw, I work on Windows.

And, if that helps, I am interested in human sequences ONLY!

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You do not need to paste them together. Just uncompress all files and keep them in one folder. makeblastdb is used to create blast indexes. These are already made so you don't need to do that step.

If you only need human proteins then you could get human protein sequneces (LINK) and create a blast index just for those using makeblastdb.

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