Thanks a lot for developing this platform with many useful tools.
I have been working on a pipeline for fosmid sequencing. I’m working in the field of functional metagenomics.
For that reason i have a request for your megablast tool. Would it be possible to set it up with the ICEberg database?
It is a curated database for mobile genetic elements.
I think you can just upload the ICEberg fasta to galaxy and run the tool NCBI BLAST+ makeblastdb to create the database. And after that use the NCBI BLAST+ blastn tool to blast (with type megablast). For the setting Subject database/sequences you can choose “BLAST database from your history”.
Is this what you need? Otherwise can you provide other details about what you are missing?
Thanks for the reponse!
Just to make sure… What you’re saying is, that i should download all files in the ICEberg database, and then upload it to galaxy. Then create a galaxy database for the data and then i should be able to do a BLAST with my sample sequences, searching through that database?