Question: Multiple fasta sequence query in a single file doing commandline blast
0
gravatar for sinumolg
22 months ago by
sinumolg10
sinumolg10 wrote:

I am doing standalone protein blast 2.6 I have a single query file contains 1000 s of fasta sequence and I want to blast it against the database. Is it possible in command line ? I am using this code but it seems stuck

blastp -query ZJ5499.txt -db Z172.db -outfmt 7  -word_size 6 -out new_out
ADD COMMENTlink modified 22 months ago by Buffo1.2k • written 22 months ago by sinumolg10

I would recommend to run the above command with only one query sequence first, then with 10 query sequences, and then with 100. How long does it take for one an for 10 queries? Only if all test runs with a small set of queries are successful, you should start with 1000 query sequences.

ADD REPLYlink written 22 months ago by piet1.6k

Make sure your 'fasta' files are indeed fasta. Your query suffix is named '.txt', and your db is named '.db'. Did you run makeblastdb command on your database fasta file?

ADD REPLYlink written 22 months ago by st.ph.n2.4k
2
gravatar for Buffo
22 months ago by
Buffo1.2k
Buffo1.2k wrote:

You have to read a complete tutorial but:

After installing blast in your computer and saving it in your path;
You need;
Database;
mi_database.fasta -> (or .faa, whatever)
-o T = save the output
-p T = is this a protein database? T= yes F = False (for nucleotide database)
formatdb -i mi_database.fasta -o T -p T   -> You have to make an index from DB, it generates 6 indexes (like mi_database.fasta.psd, etc etc) Run it on command line.

Now you have database correctly indexed and I supossed that your proteins (query) in fasta format.
this is an example of blast, but you can play with the multiple options (https://www.ncbi.nlm.nih.gov/books/NBK279675/);

blastp -query your_query.faa -db mi_database.fasta -evalue 1e-5 -outfmt 6 -out blast_result.txt
ADD COMMENTlink written 22 months ago by Buffo1.2k
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