query($sql); if($result === false){ echo "execute failed " . $mysqli->error(); echo "

wrong

"; }else{ while($row = $result->fetch_array(MYSQLI_NUM)){ global $status; list($sequence, $seqname, $status, $cutoff, $dcddn, $dcddb, $init_type) = $row; $seq_length = strlen($sequence); } } ?> ThreaDomEx Result of example

Status:

Job ID:
Protein name:
  • to be started
  • in progress
  • completed

Note:  It will take about hours to perform the prediction for your sequence. This page will refresh automatically every 10 minutes to check if the prediction is complete. Even though, we suggest users to bookmark this page or record the job ID: so that you can check back the results. In general, it takes about 4 hours to perform the domain prediction for a protein of 1000 residues; but it maybe take a longer time if there are a large number of jobs lining in the job queue.

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Status: Job_finished Download Results

Job ID:
Protein name:
Predicted Domain
  • Type:
  • Domain Number:
  • cutoff:
  • Domain(s):
Optimization and DCD Detection
  • Domain Number:
  • Domain(s):

Boundaries by user

  • Domain Number:
  • Cutoff:
  • Domain(s):

DCD Detection by user

  • Domain(s):
Status:

add segment line here

delete this segment

Domain Conservation Score

Predicted Secondary Structure

Predicted Solvent Accessibility

  • Target: visualization of the input sequence with the predicted domain segments shown in different colors;
  • Domain Conservation Score: deduced from multiple threading alignments. It allows the user to move the horizontal line to change the cutoff; or to move the vertical line to refine the boundary; or add new boundary by right-click;
  • Predicted Secondary Structure: the predicted secondary structure by PSSpred which can be used as reference to refine the boundaries;
  • Predcited Solvent Accessibilty: the predicted solvent accessibility which can be used together with predicted secondary structure to refine the boundaries;
  • Predicted domain: the domain segment predicted by the Domain Conversation Score with the default cutoff;
  • Optimization and DCD detection: boundaries optimization or discontinuous protein domains detection by the boundary cluster methods based on the predicted boundaries;
  • Boundaries by user: change or refinement of the predicted boundaries by the users. The change can be saved, rollbacked or initiated. Furthermore, it also allows the user to re-detect the discontinuous domains according to user’s editing by clicking the DCD Dectect button.
  • DCD Detection by user: the server will re-detect the discontinuous domains if there are not less than 3 segments after the user's edit. The DCD detection by the boundary clustering method is very fast. If the boundary clustering method does not detect discontinuous domains, DomEX will be used to further detect. It will take about 2-5 hours to detect the putative discontinuous domains with DomEx, which need search a library with 5,308,138 single domain sequences for each putative domain by Psi-blast.
  • s1 S1
  • s2 S2
  • s3 S3
  • s4 S4
  • s5 S5
  • s6 S6
  • s7 S7
  • s8 S8
  • s9 S9
  • s10 S10
  • s11 S11
  • s12 S12
  • domain conservation score
  • cutoff
  • segment line
  • user defined segment line
  • Strand
  • Helix
  • Coil

Sequence Alignments