<p>If you want the cds in fasta format, try:</p>

<pre><code>esearch -db nucleotide -query MT039887 | efetch -format fasta_cds_na
</code></pre>

<p>And for the proteins sequence in fasta format:</p>

<pre><code>elink -db nucleotide -target protein -id MT039887 | efetch -format fasta 
</code></pre>

CC BY-SA 4.0
2020-02-27T16:33:32.973Z
Wow!! and thank you. Thats the answer ... days like this BioSE works. @zorbax I owe you. "Acknowledgements" thank you heading your way (thats not a metaphor).
M__
CC BY-SA 4.0
2020-02-27T15:51:05.097Z
2020-02-27T15:51:05.097Z
zorbax
<p>In case you are still interested in just getting the protein ids and not sequence, you can use <code>xtract</code> like this: </p>

<pre><code>efetch -db nucleotide -format gpc -id MT039887 | xtract  -insd CDS gene product protein_id 
MT039887.1  orf1ab  orf1ab polyprotein           QHZ00388.1
MT039887.1  S       surface glycoprotein         QHZ00389.1
MT039887.1  orf3a   orf3a protein                QHZ00390.1
MT039887.1  E       envelope protein             QHZ00391.1
MT039887.1  M       membrane glycoprotein        QHZ00392.1
MT039887.1  orf6    orf6 protein                 QHZ00393.1
MT039887.1  orf7a   orf7a protein                QHZ00394.1
MT039887.1  orf8    orf8 protein                 QHZ00395.1
MT039887.1  N       nucleocapsid phosphoprotein  QHZ00396.1
MT039887.1  orf10   orf10 protein                QHZ00397.1
</code></pre>

CC BY-SA 4.0
2022-01-10T20:43:53.647Z
Thank you, this is really useful.
M__
CC BY-SA 4.0
2020-04-29T13:37:06.470Z
2020-04-29T13:37:06.470Z
vkkodali
<p>I'm downloading translated viral genomes initially via Blast - which had shortcomings - and now by <code>efetch</code>.</p>

<p>What I want to do is obtain a complete list of all translated protein ids from a nucleotide Genbank entry.</p>

<pre><code>efetch -db nucleotide -format gpc -id MT039887 | xtract -insd ....
</code></pre>

<p>The protein id and the translated gene sequences are within the <code>efetch -db nucleotide -format gpc -id MT039887</code> output ... but how do I use <code>xtract</code> to parse them?</p>

<genome><phylogeny><phylogenetics><efetch>
efetch nucleotide -> protein ids
# efetch nucleotide -> protein ids

(Asked by: username_0 on 2020-02-26)

I'm downloading translated viral genomes initially via Blast - which had shortcomings - and now by efetch.
What I want to do is obtain a complete list of all translated protein ids from a nucleotide Genbank entry.
efetch -db nucleotide -format gpc -id MT039887 | xtract -insd ....

The protein id and the translated gene sequences are within the efetch -db nucleotide -format gpc -id MT039887 output ... but how do I use xtract to parse them?

**Tags:** genome, phylogeny, phylogenetics, efetch

---

## 2 answers

### Answer by username_1 on 2020-02-27. Score: 1 | Accepted answer

If you want the cds in fasta format, try:
esearch -db nucleotide -query MT039887 | efetch -format fasta_cds_na

And for the proteins sequence in fasta format:
elink -db nucleotide -target protein -id MT039887 | efetch -format fasta

> **Comments:**
> **username_0**: Wow!! and thank you. Thats the answer ... days like this BioSE works. @zorbax I owe you. "Acknowledgements" thank you heading your way (thats not a metaphor).  

---

### Answer by username_2 on 2020-04-29. Score: 1

In case you are still interested in just getting the protein ids and not sequence, you can use xtract like this: 
efetch -db nucleotide -format gpc -id MT039887 | xtract  -insd CDS gene product protein_id 
MT039887.1  orf1ab  orf1ab polyprotein           QHZ00388.1
MT039887.1  S       surface glycoprotein         QHZ00389.1
MT039887.1  orf3a   orf3a protein                QHZ00390.1
MT039887.1  E       envelope protein             QHZ00391.1
MT039887.1  M       membrane glycoprotein        QHZ00392.1
MT039887.1  orf6    orf6 protein                 QHZ00393.1
MT039887.1  orf7a   orf7a protein                QHZ00394.1
MT039887.1  orf8    orf8 protein                 QHZ00395.1
MT039887.1  N       nucleocapsid phosphoprotein  QHZ00396.1
MT039887.1  orf10   orf10 protein                QHZ00397.1

> **Comments:**
> **username_0**: Thank you, this is really useful.  

---

