text: user3628: I want to merge/concatenate BLAST databases as suggested here.
  This is my example script that explains what I'm trying to achieve better than words can:
  #!/bin/bash
  
  for file in FAM1079.ffn FAM3228.ffn FAM6161.ffn FAM19036.ffn
  do
      echo "## Make DB for $file"
   makeblastdb -in $file -dbtype nucl &>/dev/null
      blastn -db $file  -query query_single_nucl.fasta -outfmt 6
      echo
  done
  
  echo "## Create testdb.nal..."
  blastdb_aliastool -dblist "FAM1079.ffn FAM3228.ffn FAM6161.ffn FAM19036.ffn" -dbtype nucl -title test -out testdb
  
  echo
  echo "## Test testdb.nal..."
  blastn -db testdb.nal -query query_single_nucl.fasta -outfmt 6
  
  This is the output:
  ## Make DB for FAM1079.ffn
  test_query  FAM1079_00001   100.000 1266    0   0   1   1266    1   1266    0.0 2338
  
  ## Make DB for FAM3228.ffn
  test_query  FAM3228_000001  100.000 1266    0   0   1   1266    1   1266    0.0 2338
  
  ## Make DB for FAM6161.ffn
  test_query  FAM6161_000001  100.000 1266    0   0   1   1266    1   1266    0.0 2338
  
  ## Make DB for FAM19036.ffn
  test_query  FAM19036p_000001    100.000 1266    0   0   1   1266    1   1266    0.0 2338
  
  ## Create testdb.nal...
  Created nucleotide BLAST (alias) database testdb with 12692 sequences
  
  ## Test testdb.nal...
  BLAST Database error: No alias or index file found for nucleotide database [testdb.nal] in search path [/path/to/files::]
  
  While the individual databases work, the concatenated databases don't.
  
  user3628: The problem was that the database must be specified without suffix, i.e. blastn -db testdb as opposed to blastn -db testdb.nal.
  By the way, it produces exactly the same output as
  blastn -db "FAM1079.ffn FAM3228.ffn FAM6161.ffn FAM19036.ffn" -query query_single_nucl.fasta -outfmt 6
  
  and the performance is not better.
  
original_text: 3628: <p>I want to merge/concatenate BLAST databases as suggested <a href="https://bioinformatics.stackexchange.com/questions/7386/merging-concatentating-blast-databases">here</a>.</p>
  
  <p>This is my example script that explains what I'm trying to achieve better than words can:</p>
  
  <pre><code>#!/bin/bash
  
  for file in FAM1079.ffn FAM3228.ffn FAM6161.ffn FAM19036.ffn
  do
      echo "## Make DB for <span class="math-container">$file"
   makeblastdb -in $</span>file -dbtype nucl &amp;&gt;/dev/null
      blastn -db $file  -query query_single_nucl.fasta -outfmt 6
      echo
  done
  
  echo "## Create testdb.nal..."
  blastdb_aliastool -dblist "FAM1079.ffn FAM3228.ffn FAM6161.ffn FAM19036.ffn" -dbtype nucl -title test -out testdb
  
  echo
  echo "## Test testdb.nal..."
  blastn -db testdb.nal -query query_single_nucl.fasta -outfmt 6
  </code></pre>
  
  <p>This is the output:</p>
  
  <pre><code>## Make DB for FAM1079.ffn
  test_query  FAM1079_00001   100.000 1266    0   0   1   1266    1   1266    0.0 2338
  
  ## Make DB for FAM3228.ffn
  test_query  FAM3228_000001  100.000 1266    0   0   1   1266    1   1266    0.0 2338
  
  ## Make DB for FAM6161.ffn
  test_query  FAM6161_000001  100.000 1266    0   0   1   1266    1   1266    0.0 2338
  
  ## Make DB for FAM19036.ffn
  test_query  FAM19036p_000001    100.000 1266    0   0   1   1266    1   1266    0.0 2338
  
  ## Create testdb.nal...
  Created nucleotide BLAST (alias) database testdb with 12692 sequences
  
  ## Test testdb.nal...
  BLAST Database error: No alias or index file found for nucleotide database [testdb.nal] in search path [/path/to/files::]
  </code></pre>
  
  <p>While the individual databases work, the concatenated databases don't.</p>
   3628: <p>The problem was that the database must be specified without suffix, i.e. <code>blastn -db testdb</code> as opposed to <code>blastn -db testdb.nal</code>.</p>
  
  <p>By the way, it produces exactly the same output as</p>
  
  <pre><code>blastn -db "FAM1079.ffn FAM3228.ffn FAM6161.ffn FAM19036.ffn" -query query_single_nucl.fasta -outfmt 6
  </code></pre>
  
  <p>and the performance is not better.</p>
  