page_title: Phyre
section_title: Alignment view
hierarchical_section_title: Phyre / Standard usage / Alignment view
context_page_description: Phyre and Phyre2 are free web-based services for protein structure prediction. Phyre is among the most popular methods for protein structure prediction having been cited over 1500 times. Like other remote homology recognition techniques, it is able to regularly generate reliable protein models when other widely used methods such as PSI-BLAST cannot. Phyre2 has been designed to ensure a user-friendly interface for users inexpert in protein structure prediction methods. Its development is funded by the Biotechnology and Biological Sciences Research Council.
context_section_description: 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.
caption: Example Phyre2 detailed view of the alignment between a user sequence and a known protein structure.
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