I am currently exploring the BLAST program, just for testing purpose i generated two FASTA files, containing two genes A and B, such that B is just a motif of repeated 'G's that occurs in A.
So by my understanding BLAST should find the local alignment of B in A easily? But the program returns 'No hits found'? Maybe I am doing something wrong here?
I executed the following:
makeblastdb -in A.fna -dbtype 'nucl' makeblastdb -in B.fna -dbtype 'nucl' blastn -db A.fna -query B.fna
output of blastn:
BLASTN 2.7.1+ 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: A.fna 1 sequences; 64 total letters Query= B Length=12 ***** 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: 480 Database: A.fna Posted date: May 3, 2018 5:17 PM Number of letters in database: 64 Number of sequences in database: 1 Matrix: blastn matrix 1 -2 Gap Penalties: Existence: 0, Extension: 2.5
Thanks for any suggestions (: