<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>

CC BY-SA 4.0
2022-12-06T10:19:20.047Z
This was helpful, thank you! What would you suggest I use as identifier to filter more specifically? I tried substituting "aminoacyl-tRNA\ hydrolase" with gene-ID (61281026) but that doesn't seem to work.
Vjon
CC BY-SA 4.0
2022-12-06T20:01:57.450Z
@Vjon I would suggest trying an [NCBI taxid](https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi) in place of the species name.
Maximilian Press
CC BY-SA 4.0
2022-12-05T21:31:48.227Z
2022-12-05T21:31:48.227Z
Maximilian Press
<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>

CC BY-SA 4.0
2022-12-04T23:40:51.977Z
Hi how does the list of 140 gene you are interested in look like? do you have gene accessions, or Ids or just gene symbols?, ie symbol: BRCA1 ; id : 
    672 ; accsession NC_000017.11 , are all the same gene.
user12256545
CC BY-SA 4.0
2022-12-05T06:36:59.303Z
what output do you get from your commands? nothing, an error, the wrong gene?
Maximilian Press
CC BY-SA 4.0
2022-12-05T09:51:27.340Z
Yes, please [edit] your question and add a few lines of your input file. Presumably, you have a list of genes, so please show us the list so we can understand the input format.
terdon
CC BY-SA 4.0
2022-12-06T09:34:52.077Z
@user12256545 Right now I have the list on a word-document with locus name and gene-ID (that would be "pth" and 61281026 for aminoacyl-tRNA hydrolase). All genes seem to have the same accession nr. so that won't be useful unfortunately.
Vjon
<fasta><phylogenetics><data-download><sequence>
Downloading genes from NCBI in fasta format
# Downloading genes from NCBI in fasta format

(Asked by: username_0 on 2022-12-04)

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 :)

**Tags:** fasta, phylogenetics, data-download, sequence
> **Comments:**
> **username_1**: Hi how does the list of 140 gene you are interested in look like? do you have gene accessions, or Ids or just gene symbols?, ie symbol: BRCA1 ; id :      672 ; accsession NC_000017.11 , are all the same gene.  
> **username_2**: what output do you get from your commands? nothing, an error, the wrong gene?  
> **username_3**: Yes, please [edit] your question and add a few lines of your input file. Presumably, you have a list of genes, so please show us the list so we can understand the input format.  
> **username_0**: @user12256545 Right now I have the list on a word-document with locus name and gene-ID (that would be "pth" and 61281026 for aminoacyl-tRNA hydrolase). All genes seem to have the same accession nr. so that won't be useful unfortunately.  

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## 1 answers

### Answer by username_2 on 2022-12-05. Score: 2

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.

> **Comments:**
> **username_0**: This was helpful, thank you! What would you suggest I use as identifier to filter more specifically? I tried substituting "aminoacyl-tRNA\ hydrolase" with gene-ID (61281026) but that doesn't seem to work.  
> **username_2**: @Vjon I would suggest trying an [NCBI taxid](https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi) in place of the species name.  

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