<p>I found a definition:
&quot;A pattern is thus a qualitative description of a motif in terms of amino acid sequence. The concept of a profile extends this concept, allowing a quantitative description of a motif, by assigning probabilities to the occurrence of a particular amino acid at each position of a motif.&quot;</p>
<p>This is example of profile in prosite</p>
<pre><code>Hits for all PROSITE (release 2022_04) motifs on sequence P98073 [UniProtKB/Swiss-Prot]:
Example of profile
PS50024   SEA   SEA domain profile :
54 - 169:   score = 32.979
QSHEARATFKITsGVTYNPNLQDKLSVDFKVLAFDLQQMIDEIFLSSNLKNEYKNSRVLQ
FEN--GSIIVVFDLFFAQWVSD--ENVKEELIQGLEANKssQLVTFHIDLNSVDILDKLT

This is example of pattern in Prosite
PS01209   LDLRA_1   LDL-receptor class A (LDLRA) domain signature :
197 - 221:     [confidence level: (0)]  CIkadlf.CDgevNCpdgsDEDnkm..C
</code></pre>
<ol>
<li>What is the difference in that case? So in profile I have probabilities (in definition I have &quot;profile extends this concept, allowing a quantitative description of a motif, by assigning probabilities to the occurrence of a particular amino acid&quot;. I don't see any probabilities in that sequence.</li>
<li>What does it mean &quot;-&quot; in profiles? Maybe any aminoacid or gap?</li>
<li>Why I have sometimes lowercase letter and uppercase letter in profile and pattern? I don't get it. It's a probability?</li>
<li>What is more important profile or pattern?</li>
</ol>

CC BY-SA 4.0
2022-10-18T18:37:00.943Z
Hi @MrMorgotheron and welcome. From my point of view its a good question, but a few too many questions, albeit I could be wrong. The "-" definitely means an indel, so you can remove that question to help focus the question more.
M__
CC BY-SA 4.0
2022-10-20T04:50:53.570Z
I think this was already answered on a different SE site: https://biology.stackexchange.com/questions/46751/difference-between-motifs-domains-patterns-signatures-and-profiles
Maximilian Press
CC BY-SA 4.0
2022-10-22T11:02:40.643Z
This publication explains it nicely: https://academic.oup.com/bib/article/3/3/265/239712?login=false
Avamys
<proteins><prosite>
What is the difference between profile and pattern in Prosite?
# What is the difference between profile and pattern in Prosite?

(Asked by: username_0 on 2022-10-18)

I found a definition:
"A pattern is thus a qualitative description of a motif in terms of amino acid sequence. The concept of a profile extends this concept, allowing a quantitative description of a motif, by assigning probabilities to the occurrence of a particular amino acid at each position of a motif."
This is example of profile in prosite
Hits for all PROSITE (release 2022_04) motifs on sequence P98073 [UniProtKB/Swiss-Prot]:
Example of profile
PS50024   SEA   SEA domain profile :
54 - 169:   score = 32.979
QSHEARATFKITsGVTYNPNLQDKLSVDFKVLAFDLQQMIDEIFLSSNLKNEYKNSRVLQ
FEN--GSIIVVFDLFFAQWVSD--ENVKEELIQGLEANKssQLVTFHIDLNSVDILDKLT

This is example of pattern in Prosite
PS01209   LDLRA_1   LDL-receptor class A (LDLRA) domain signature :
197 - 221:     [confidence level: (0)]  CIkadlf.CDgevNCpdgsDEDnkm..C


What is the difference in that case? So in profile I have probabilities (in definition I have "profile extends this concept, allowing a quantitative description of a motif, by assigning probabilities to the occurrence of a particular amino acid". I don't see any probabilities in that sequence.
What does it mean "-" in profiles? Maybe any aminoacid or gap?
Why I have sometimes lowercase letter and uppercase letter in profile and pattern? I don't get it. It's a probability?
What is more important profile or pattern?

**Tags:** proteins, prosite
> **Comments:**
> **username_1**: Hi @MrMorgotheron and welcome. From my point of view its a good question, but a few too many questions, albeit I could be wrong. The "-" definitely means an indel, so you can remove that question to help focus the question more.  
> **username_2**: I think this was already answered on a different SE site: https://biology.stackexchange.com/questions/46751/difference-between-motifs-domains-patterns-signatures-and-profiles  
> **username_3**: This publication explains it nicely: https://academic.oup.com/bib/article/3/3/265/239712?login=false  

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