I am trying to reproduce locally on my computer what I get running mirbase on their website using BLAST. The search sequences is: mature miRNAs which I had downloaded on my computer and make it as a BLAST database with command:
./makeblastdb -in /home/marianoavino/Downloads/mature.fa -dbtype 'nucl' -out /home/marianoavino/Downloads/mature
then on mirbase I see they use an e-value of 10, which I leave locally. On mirbase at the end of the analysis they give you these parameter setting:
Search algorithm: BLASTN Sequence database: mature Evalue cutoff: 10 Max alignments: 100 Word size: 4 Match score: +5 Mismatch penalty: -4
and this is the command line I use on my computer for BLAST
./blastn -db /home/marianoavino/Downloads/mature -evalue 10 -word_size 4 -query /home/marianoavino/Downloads/testinputblast.fasta -task "blastn" -out /home/marianoavino/Downloads/testBLast.out
The results of the two analysis are different, with mirbase finding much more stuff than local BLAST.
Do you have any idea on which parameters I should use on local blast command line to match those listed mirbase parameters in order to get the same answer?