sequence into the Phyre or Phyre2 submission form, a user will typically wait between 30 minutes and several hours (depending on factors such as sequence length, number of homologous sequences and frequency and length of insertions and deletions) for a prediction to complete. An email containing summary information and the predicted structure in PDB format are sent to the user together with a link to a web page of results. The Phyre2 results screen is divided into three main sections, described below. Secondary structure and disorder prediction The user-submitted protein sequence is first scanned against a large sequence database using PSI-BLAST. The profile generated by PSI-BLAST is then processed by the neural network secondary structure prediction program PsiPred and the protein disorder predictor Disopred. The predicted presence of alpha-helices, beta-strands and disordered regions is shown graphically together with a color-coded confidence bar. Domain analysis Many proteins contain multiple protein domains. Phyre2 provides a table of template matches color-coded by confidence and indicating the region of the user sequence matched. This can aid in the determination of the domain composition of a protein. Detailed template information The main results table in Phyre2 provides confidence estimates, images and links to the three-dimensional predicted models and information derived from either Structural Classification of Proteins database (SCOP) or the Protein Data Bank (PDB) depending on the source of the detected template. For each match a link takes the user to a detailed view of the alignment between the user sequence and the sequence of known three-dimensional structure. Alignment view The detailed alignment view permits a user to examine individual aligned residues, matches between predicted and known secondary structure elements and the ability to toggle information regarding patterns of sequence conservation and secondary structure confidence. In addition Jmol is used to permit interactive 3D viewing of the protein model. Improvements in Phyre2 Phyre2 uses a fold library that is updated weekly as new structures are solved. It uses a more up-to-date interface and offers additional functionality over the Phyre server as described below. Additional functionality Batch processing The batch processing feature permits users to submit more than one sequence to Phyre2 by uploading a file of sequences in FASTA format. By default, users have a limit of 100 sequences in a batch. This limit can be raised by contacting the administrator. Batch jobs are processed in the background on free computing power as it becomes