<p>I think MEME is a good tool for your purpose, but there are others as well. I can think of <a href="http://www.ebi.ac.uk/interpro/interproscan.html" rel="nofollow noreferrer">InterProScan</a> for example (although I am not sure if it is really <em>de novo</em>). <a href="https://molbiol-tools.ca/Motifs.htm" rel="nofollow noreferrer">Here</a> a summary of available tools.</p>

CC BY-SA 4.0
2018-12-04T08:53:41.757Z
2018-12-04T08:53:41.757Z
benn
<p>I am trying to build a features matrix to be used for Random Forest based classification. I'd like to add, as features, short motifs which are common to all the protein sequences belonging to a specific gene family.</p>

<p>I tried to use MEME but I'd like to know if there are also other good tools (online or command line). Keep in mind I have more than 10.000 sequences and that I prefer short motifs (3/4 aa long).</p>

<proteins><sequence-analysis><motifs><machine-learning>
De novo motif discovery in protein sequences
# De novo motif discovery in protein sequences

(Asked by: username_0 on 2018-12-03)

I am trying to build a features matrix to be used for Random Forest based classification. I'd like to add, as features, short motifs which are common to all the protein sequences belonging to a specific gene family.

I tried to use MEME but I'd like to know if there are also other good tools (online or command line). Keep in mind I have more than 10.000 sequences and that I prefer short motifs (3/4 aa long).

**Tags:** proteins, sequence-analysis, motifs, machine-learning

---

## 1 answers

### Answer by username_1 on 2018-12-04. Score: 3

I think MEME is a good tool for your purpose, but there are others as well. I can think of [InterProScan](http://www.ebi.ac.uk/interpro/interproscan.html) for example (although I am not sure if it is really *de novo*). [Here](https://molbiol-tools.ca/Motifs.htm) a summary of available tools.


---

