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 parameters

Search algorithm:
Sequence database:
Evalue cutoff:
Max alignments:
Word size:
Match score:
Mismatch penalty:

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?


1 Answer 1


The main problem I could identify is that your scoring matrix is not the same; as you said miRbase uses match score of +5 and mismatch penalty of -4.

The BLASTN defaults can be found here. However, I ran the local BLAST using the exact command that you mentioned and the default values that it used were:
reward = +1
penalty = -2

Matrix: blastn matrix 1 -2
Gap Penalties: Existence: 0, Extension: 2.5

The other reasons could be the difference in the database itself (the sequences used) or the version of BLAST used in the two cases.


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