Answers.Body: <p>As per PROSITE database manual:</p>
  <blockquote>
  <p>Unlike patterns, profiles are usually not confined to small regions
  with high sequence similarity. Rather they attempt to characterize a
  protein family or domain over its entire length. This can lead to
  specific problems not arising with PROSITE patterns. With a profile
  covering conserved as well as divergent sequence regions, there is a
  chance to obtain a significant similarity score even with a partially
  incorrect alignment. This possibility is taken into account by our
  quality evaluation procedures. <strong>In order to be acceptable, a profile
  must not only assign high similarity scores to true motif occurrences
  and low scores to false matches.</strong> In addition, it should correctly
  align those residues having analogous functions or structural
  properties according to experimental data.</p>
  <p><strong>Profiles are supposed to be more sensitive and more robust than</strong>
  <strong>patterns because they provide discriminatory weights not only for the</strong>
  <strong>residues already found at a given position of a motif but also for</strong>
  <strong>those not yet found.</strong> The weights for those not yet found are
  extrapolated from the observed amino acid compositions using empiric
  knowledge about amino acid substitutability.</p>
  </blockquote>
  <p>Given the less biased and somewhat more balanced result provided by a profile I would say that the sequence contains two motifs that correspond to a PS51408 TRANSFERRIN_LIKE_4 Transferrin-like domain profile and provide the bitscore and e-value for the match.</p>
  <p>Best,</p>
  <p>av</p>
  
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Answers.CreationDate: 2022-11-02T19:43:23.747Z
Answers.LastActivityDate: 2022-11-02T19:43:23.747Z
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Body: <p>For example I checked motifs in Transferrin P02787  <a href="https://prosite.expasy.org/cgi-bin/prosite/ScanView.cgi?scanfile=816050634835.scan.gz" rel="nofollow noreferrer">https://prosite.expasy.org/cgi-bin/prosite/ScanView.cgi?scanfile=816050634835.scan.gz</a></p>
  <p>I have
  hits by profiles: [2 hits (by 1 profile) on 1 sequence]
  and
  hits by patterns: [5 hits (by 3 distinct patterns) on 1 sequence]</p>
  <p>Can I say that I detect <strong>4 different motifs</strong>? One motif is searched by profile searching (PS51408   TRANSFERRIN_LIKE_4   Transferrin-like domain profile two times) and three motifs are searched by pattern searching (PS00205   TRANSFERRIN_LIKE_1   Transferrin-like domain signature 1, PS00206   TRANSFERRIN_LIKE_2   Transferrin-like domain signature 2 two times, PS00207   TRANSFERRIN_LIKE_3   Transferrin-like domain signature 3 two times).</p>
  <p>All the motifs found are equal to 7? Is it right? Can I talk about the different motifs found by the profile and pattern, or are they the same in some way?</p>
  
Tags: <motifs><prosite>
Title: How to count number of motifs in Prosite?
ThreadText: # How to count number of motifs in Prosite?
  
  (Asked by: username_0 on 2022-10-30)
  
  For example I checked motifs in Transferrin P02787 <https://prosite.expasy.org/cgi-bin/prosite/ScanView.cgi?scanfile=816050634835.scan.gz>
  
  I have
  hits by profiles: [2 hits (by 1 profile) on 1 sequence]
  and
  hits by patterns: [5 hits (by 3 distinct patterns) on 1 sequence]
  
  Can I say that I detect **4 different motifs**? One motif is searched by profile searching (PS51408 TRANSFERRIN\_LIKE\_4 Transferrin-like domain profile two times) and three motifs are searched by pattern searching (PS00205 TRANSFERRIN\_LIKE\_1 Transferrin-like domain signature 1, PS00206 TRANSFERRIN\_LIKE\_2 Transferrin-like domain signature 2 two times, PS00207 TRANSFERRIN\_LIKE\_3 Transferrin-like domain signature 3 two times).
  
  All the motifs found are equal to 7? Is it right? Can I talk about the different motifs found by the profile and pattern, or are they the same in some way?
  
  **Tags:** motifs, prosite
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-11-02. Score: 2
  
  As per PROSITE database manual:
  
  > Unlike patterns, profiles are usually not confined to small regions
  > with high sequence similarity. Rather they attempt to characterize a
  > protein family or domain over its entire length. This can lead to
  > specific problems not arising with PROSITE patterns. With a profile
  > covering conserved as well as divergent sequence regions, there is a
  > chance to obtain a significant similarity score even with a partially
  > incorrect alignment. This possibility is taken into account by our
  > quality evaluation procedures. **In order to be acceptable, a profile
  > must not only assign high similarity scores to true motif occurrences
  > and low scores to false matches.** In addition, it should correctly
  > align those residues having analogous functions or structural
  > properties according to experimental data.
  >
  > **Profiles are supposed to be more sensitive and more robust than**
  > **patterns because they provide discriminatory weights not only for the**
  > **residues already found at a given position of a motif but also for**
  > **those not yet found.** The weights for those not yet found are
  > extrapolated from the observed amino acid compositions using empiric
  > knowledge about amino acid substitutability.
  
  Given the less biased and somewhat more balanced result provided by a profile I would say that the sequence contains two motifs that correspond to a PS51408 TRANSFERRIN\_LIKE\_4 Transferrin-like domain profile and provide the bitscore and e-value for the match.
  
  Best,
  
  av
  
  
  ---
  
  