I'm searching for short sequences in nt. By short, I mean 10-20 bases. When I run blastn, I get no results, regardless of my -evalue settings. Here's the test sequence:
And I run BLAST as follows:
./blastn -db nt -remote -query test2.seq -task "megablast" -out test2.out
With the default evalue settings, I should get a lot of hits, but I get none. I've verified this on the NCBI web service but it informs me that adjustments have been made to the parameters to accommodate my short search. I want to make these adjustment from the command line, but I'm not sure where to start.
Here's my output:
BLASTN 2.2.26+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,environmental samples or phase 0, 1 or 2 HTGS sequences) 16,169,102 sequences; 41,381,280,968 total letters Query= ponzr1 Length=18 RID: XU4WV327016 ***** No hits found ***** Lambda K H 1.33 0.621 1.12 Gapped Lambda K H 1.28 0.460 0.850 Effective search space used: 123416233314 Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,environmental samples or phase 0, 1 or 2 HTGS sequences) Posted date: Jun 15, 2012 10:12 AM Number of letters in database: 41,381,280,968 Number of sequences in database: 16,169,102 Matrix: blastn matrix 1 -2 Gap Penalties: Existence: 0, Extension: 2.5
Kevin, thank you so much for this answer. This option worked and lifted me from a pit of despair =)