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 hope to hear from you.
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?
How many files you need to download from ICEberg I dont know. But I see you can select multiple files in NCBI BLAST+ makeblastdb at once.
- Create a fasta file(s) with all references you want to search trough
- Upload this file(s) to galaxy
- Run tool NCBI BLAST+ makeblastdb with your fasta as input
- Upload your fasta that you want to blast
- Open NCBI BLAST+ blastn (for nucleotide, if you have protein you will use blastp)
- Select your fasta with sequences that you want to blast, select “BLAST database from your history” and select the database you created in step 3.
- Select all settings that you want, I your case you want to at least select megblast (which is default already)