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:
>ponzr
CGCGGTAAAACACATTTG
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
...