Dear Galaxy users, Is the only way to blastp in Galaxy is against a database from your own history (meaning downloading from https://www.uniprot.org/downloads , uploading to your history, make protein blast db, and then blast) or is there somehow access to these databases in the tool itself? I want…

2025 Update!! The NR index has been available in BLAST+ tools at all public UseGalaxy servers since early 2020! Not sure which to use? Start here: https://galaxyproject.org → Regions

[image] kml: Is the only way to blastp in Galaxy is against a database from your own history Yes, this is true at public Galaxy servers. If running your own Galaxy, native indexes can be installed. NCBI hosts pre-built indexes or you can create these yourself. Should you be interested in doi…

Thanks for your reply and for checking these databases. where can I download the NR database?

The fasta and pre-indexed versions of NR can be found here: ftp://ftp.ncbi.nlm.nih.gov/blast/db/ This is a large database that will probably fail indexing (using makeblastdb) for exceeding memory or runtime resources at public servers (including all usegalaxy.* servers). It is best used in your own…

thanks for the link, but which one there I should download? also I’m not sure what do you mean by using my own galaxy? maybe I can ask the administrator to allocate more memory to this specific process?

[image] kml: thanks for the link, but which one there I should download? This depends on if you want to create your own indexes or use the pre-built indexes. The fasta version of the data and the pre-built indexes are both available. Review the README at this location to learn about both. …

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blastp against nr database

mapping, blast, blastp

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