Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-18T18:37:00.943Z
Comments.Text: 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.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-20T04:50:53.570Z
Comments.Text: 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
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-22T11:02:40.643Z
Comments.Text: This publication explains it nicely: https://academic.oup.com/bib/article/3/3/265/239712?login=false
Comments.UserDisplayName: Avamys
Tags: <proteins><prosite>
Title: What is the difference between profile and pattern in Prosite?
ThreadText: # 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
  
  ```
  
  1. 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.
  2. What does it mean "-" in profiles? Maybe any aminoacid or gap?
  3. Why I have sometimes lowercase letter and uppercase letter in profile and pattern? I don't get it. It's a probability?
  4. What is more important profile or pattern?
  
  **Tags:** proteins, prosite
  
  > **Comments:**
  > **username_1**: Hi @username_0 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  
  
  ---
  
  ## 0 answers
  
  