text: user16594: I'm pretty new in bioinformatics.
  I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I'd rather do this through via code than download each gene manually from the NCBI database.
  The genes belong to 2 different organisms (bacteria) I have chosen, most of them are found in both organisms and some are specific to one or the other bacterium.
  I've tried running this code which I found here: https://www.ncbi.nlm.nih.gov/books/NBK179288/
  esearch -db nucleotide -query "aminoacyl-tRNA\ hydrolase" | efetch -format fasta
  
  The gene of interest being aminoacyl-tRNA hydrolase here. But I don't know how to filter it for the specific organism, Neisseria meningitidis. Tried running this, without luck:
  esearch -db nucleotide -query "aminoacyl-tRNA\ hydrolase" | efilter -organism [Neisseria meningitidis] | efetch -format fasta
  
  Appreciate any help :)
  
  user2108: If I put the species name in quotes, I get expected (by me) output:
  % esearch -db nucleotide -query "aminoacyl-tRNA\ hydrolase" | efilter -organism "Neisseria meningitidis" | efetch -format fasta
  # outputs:
  >NZ_JWNU01000010.1 Neisseria meningitidis strain Nm440716 Scaffold10, whole genome shotgun sequence
  GACCGCCTATTCGCTTGCCGCCGGCGGCCCCATCATGCAGGCAGGATTACACGCCTTCACACTCGTACCC
  # [snip, tons of output]
  
  Note that filtering down to only N. meningitidis still leaves all of the different sequenced accessions of this species, such that you will still have a lot of different annotated copies of this gene. You will need to filter more specifically to reduce that.
  
original_text: 16594: <p>I'm pretty new in bioinformatics.</p>
  <p>I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I'd rather do this through via code than download each gene manually from the NCBI database.</p>
  <p>The genes belong to 2 different organisms (bacteria) I have chosen, most of them are found in both organisms and some are specific to one or the other bacterium.</p>
  <p>I've tried running this code which I found here: <a href="https://www.ncbi.nlm.nih.gov/books/NBK179288/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/books/NBK179288/</a></p>
  <pre><code>esearch -db nucleotide -query &quot;aminoacyl-tRNA\ hydrolase&quot; | efetch -format fasta
  </code></pre>
  <p>The gene of interest being aminoacyl-tRNA hydrolase here. But I don't know how to filter it for the specific organism, Neisseria meningitidis. Tried running this, without luck:</p>
  <pre><code>esearch -db nucleotide -query &quot;aminoacyl-tRNA\ hydrolase&quot; | efilter -organism [Neisseria meningitidis] | efetch -format fasta
  </code></pre>
  <p>Appreciate any help :)</p>
   2108: <p>If I put the species name in quotes, I get expected (by me) output:</p>
  <pre><code>% esearch -db nucleotide -query &quot;aminoacyl-tRNA\ hydrolase&quot; | efilter -organism &quot;Neisseria meningitidis&quot; | efetch -format fasta
  # outputs:
  &gt;NZ_JWNU01000010.1 Neisseria meningitidis strain Nm440716 Scaffold10, whole genome shotgun sequence
  GACCGCCTATTCGCTTGCCGCCGGCGGCCCCATCATGCAGGCAGGATTACACGCCTTCACACTCGTACCC
  # [snip, tons of output]
  </code></pre>
  <p>Note that filtering down to only <em>N. meningitidis</em> still leaves all of the different sequenced accessions of this species, such that you will still have a lot of different annotated copies of this gene. You will need to filter more specifically to reduce that.</p>
  