text: user16327: 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?
  
  user14212: 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
  
original_text: 16327: <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>
   14212: <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>
  