<p>If I understand your question correctly, then you can use the Pfam proteom search to get the data you are looking for.</p>

<p>Go to the </p>

<blockquote>
  <p>Pfam website -> Browse -> select the letter D from proteoms category
  -> D. rerio</p>
</blockquote>

<p>There you can find a download link under the section <code>Domain composition</code>: </p>

<blockquote>
  <p>You can download a list of all regions for this proteome from our FTP
  site.</p>
</blockquote>

<p>The download link seems to be bound to the species ID and if you want to automate your data retrieval you may be able to simply download the file from there in your python script.</p>

CC BY-SA 4.0
2018-08-24T13:00:07.340Z
Exactly what I needed. Although, the species ID is not that informative but I think I can manage that easier in the future. Thank you!
Đorđe Relić
CC BY-SA 4.0
2018-08-24T13:06:14.753Z
One thing to note though is that `seq_info` at Pfam is retrieved from UniProt database so in order to retrieve that data, one needs to make a mapping from list of proteoms and `uniprot.gz` file at the Pfam ftp server. The tricky part comes if the two databases are not synced. But that's not an issue that should be discussed here.
Đorđe Relić
CC BY-SA 4.0
2018-08-24T11:48:20.223Z
2018-08-24T11:53:48.357Z
2018-08-24T11:53:48.357Z
voiDnyx
<p>I'm interested in all proteins that are in any way associated with <em>Danio rerio</em>. I decided to look them up at Pfam data base and when I just make a keyword search, I get a a nice list which looks like this <a href="http://pfam.xfam.org/search/keyword?query=danio%20rerio&amp;submit=Submit" rel="nofollow noreferrer">http://pfam.xfam.org/search/keyword?query=danio+rerio&amp;submit=Submit</a>. 
Important thing to note is that most of the associations of these protein families can be found in <strong>seq_info</strong> column.</p>

<p>My question is: how to extract that list from a python script? Moreover, I want to make a script that when run, will fetch the latest release, filter out the proteins that cannot be found in <em>D. rerio</em> and do some additional processing.</p>

<p>I've been searching for ways to directly download files from Pfam ftp server and mine for the proteins that are associated with <em>D. rerio</em>, however, I didn't find a single way to do it. I simply cannot see where do they store the information about species in which the protein can be found.</p>

<p>I would like to retrieve everything about protein families of interest, because the next step I will need to do is to find the DNA binding proteins and for finding a way to filter out the ones of no interest, I would liketo have as much data as possible. </p>

<python><public-databases>
Get results of keyword search on Pfam via python script
# Get results of keyword search on Pfam via python script

(Asked by: username_0 on 2018-08-23)

I'm interested in all proteins that are in any way associated with *Danio rerio*. I decided to look them up at Pfam data base and when I just make a keyword search, I get a a nice list which looks like this [http://pfam.xfam.org/search/keyword?query=danio+rerio&submit=Submit](http://pfam.xfam.org/search/keyword?query=danio%20rerio&submit=Submit).
Important thing to note is that most of the associations of these protein families can be found in **seq\_info** column.

My question is: how to extract that list from a python script? Moreover, I want to make a script that when run, will fetch the latest release, filter out the proteins that cannot be found in *D. rerio* and do some additional processing.

I've been searching for ways to directly download files from Pfam ftp server and mine for the proteins that are associated with *D. rerio*, however, I didn't find a single way to do it. I simply cannot see where do they store the information about species in which the protein can be found.

I would like to retrieve everything about protein families of interest, because the next step I will need to do is to find the DNA binding proteins and for finding a way to filter out the ones of no interest, I would liketo have as much data as possible.

**Tags:** python, public-databases

---

## 1 answers

### Answer by username_1 on 2018-08-24. Score: 1 | Accepted answer

If I understand your question correctly, then you can use the Pfam proteom search to get the data you are looking for.

Go to the

> Pfam website -> Browse -> select the letter D from proteoms category
> -> D. rerio

There you can find a download link under the section `Domain composition`:

> You can download a list of all regions for this proteome from our FTP
> site.

The download link seems to be bound to the species ID and if you want to automate your data retrieval you may be able to simply download the file from there in your python script.

> **Comments:**
> **username_0**: Exactly what I needed. Although, the species ID is not that informative but I think I can manage that easier in the future. Thank you!  
> **username_0**: One thing to note though is that `seq_info` at Pfam is retrieved from UniProt database so in order to retrieve that data, one needs to make a mapping from list of proteoms and `uniprot.gz` file at the Pfam ftp server. The tricky part comes if the two databases are not synced. But that's not an issue that should be discussed here.  

---

