Question: Trying to reproduce mirbase results locally with BLAST
1
gravatar for avino
21 months ago by
avino10
avino10 wrote:

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: 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?

blast • 868 views
ADD COMMENTlink written 21 months ago by avino10
2

-task blastn-short for very short sequences

ADD REPLYlink written 21 months ago by Buffo1.6k
1
blastn -query [file] -db [file] -task blastn-short -word_size 4 -penalty -4 -reward 5 -dust no -soft_masking false -num_alignments 100
ADD REPLYlink written 21 months ago by a.zielezinski8.7k
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