Body: <p>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:</p>
  
  <pre><code>./makeblastdb -in /home/marianoavino/Downloads/mature.fa -dbtype 'nucl' -out /home/marianoavino/Downloads/mature
  </code></pre>
  
  <p>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:</p>
  
  <pre><code>Search parameters
  
  Search algorithm:   BLASTN   
  Sequence database: mature  
  Evalue cutoff: 10  
  Max alignments: 100  
  Word size: 4  
  Match score: +5  
  Mismatch penalty: -4  
  </code></pre>
  
  <p>and this is the command line I use on my computer for BLAST</p>
  
  <pre><code>./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
  </code></pre>
  
  <p>The results of the two analysis are different, with mirbase finding much more stuff than local BLAST.</p>
  
  <p>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?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-28T23:09:05.677Z
Comments.Text: You don't mention which version of BLAST you have installed locally and if that matches the web version.  Can you also provide a link the web version of mirbase?
Comments.UserDisplayName: Bioathlete
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-04T22:00:27.200Z
Comments.Text: BLAST version on my computer is 2.7.1+, the link for mirbase is http://mirbase.org/search.shtml, not sure which version of Blast they use. Thanks.
Comments.UserDisplayName: Mariano Avino
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-04T22:18:15.253Z
Comments.Text: I would start with finding out what version of BLAST they use and then make sure you have the same one.  Then I would look at the man pages for BLAST and get the match score and mismatch penalty set.  Also even though it doesn't seem like it should matter the max alignments setting can change the results so I would have BLASt do that filtering for you as well.
Comments.UserDisplayName: Bioathlete
Tags: <blast>
Title: Mirbase and blast locally
ThreadText: # Mirbase and blast locally
  
  (Asked by: username_0 on 2017-11-28)
  
  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/username_0/Downloads/mature.fa -dbtype 'nucl' -out /home/username_0/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/username_0/Downloads/mature -evalue 10 -word_size 4 -query /home/username_0/Downloads/testinputblast.fasta -task "blastn" -out /home/username_0/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?
  
  **Tags:** blast
  
  > **Comments:**
  > **username_1**: You don't mention which version of BLAST you have installed locally and if that matches the web version.  Can you also provide a link the web version of mirbase?  
  > **username_0**: BLAST version on my computer is 2.7.1+, the link for mirbase is http://mirbase.org/search.shtml, not sure which version of Blast they use. Thanks.  
  > **username_1**: I would start with finding out what version of BLAST they use and then make sure you have the same one.  Then I would look at the man pages for BLAST and get the match score and mismatch penalty set.  Also even though it doesn't seem like it should matter the max alignments setting can change the results so I would have BLASt do that filtering for you as well.  
  
  ---
  
  ## 0 answers
  
  