Hello biostars,

I have a FASTA file of about 300 kbp & I have several sequences (400 bp - 800 bp) that I want to search in there.

I tried using BLAST, but I couldn't find the option to allow me to upload my own FASTA file in the Search Set box.

I tried this:
http://www.ebi.ac.uk/Tools/psa/emboss_water/nucleotide.html

The EMBOSS water stops and lists the first hit, but the sequences occur multiple times throughout the FASTA files.

Does anyone have any other software or other ideas? Thank you!


You can use the command line version of blast+ to create a database out of your sequences (using `makeblastdb`) and then blast your query sequence against this database. It is not possible to do what you want on the web.