I am trying to BLAST several sequences using the latest command line-based BLAST+ on a Linux machine. Whatever I do, I get the unfortunate "No hits found" message.
I randomly chose some of my sequences and tried the web-based API. To my surprise I received dozens of results for almost all of them with identities higher than 92%!
Here is one example sequence: CAGTTTNCATTTTATAACT
On the web, I simply navigate to 'blastn' (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and I leave all settings unchanged (it uses megablast and the nt database collection), and I receive many hits for the sequence above.
When I try the shell-based BLAST on the same sequence above, I get nothing!
I have tried both a remote search:
blastn -task megablast -db nt -remote -query test_sequence.fasta -out remote_blast_test_megablast_output.txt blastn -task blastn-short -db nt -remote -query test_sequence.fasta -out remote_blast_test_blastnshort_output.txt
...And also a local search on my own computer:
blastn -task megablast -db /home/blast_databases/nt -query test_sequence.fasta -out blast_test_megablast_output_localdatabase.txt blastn -task blastn-short -db /home/blast_databases/nt -query test_sequence.fasta -out blast_test_blastnshort_output_localdatabase.txt
I have also considered adding the
-perc_identity 92 parameters, and those have also solved nothing.
How can I reproduce the same results that BLAST's web API returns?
I have so far gotten closer to the web results by specifying:
- word_size 7
- evalue 1000 (on the command line version, it was set to 10 by default!!)
- task -blastn-short