Use BLAST's search on your own FASTA?

Question

[orlando.wong]

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!

Answer 1

[Ram]

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.

Answer 2

[biofalconch]

Ok, what I make of that tool is that it is used to just align TWO sequences, so naturally it just ignores the rest. Adding to @Ram 's answer, you want to create a database for your fasta using makeblastdb (is as easy as makeblastdb -in file.fa -dbtype nucl -out database), once you have your database set, you can go on and run blastn (blastn -query file.fa -db database -out file.out -outfmt 6). Now, it depends on how you want your output (option -outfmt), I recommend reading more. This will give you a text output that can be more easily searched than using webtools. Hope it helps :)

[orlando.wong]

Thanks so much for the BLAST command line commands. Was able to run it blazing fast in less than 0.5 seconds!