--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+<meta charset="UTF-8">
+<title>SIFTS Mapping</title>
+</head>
+<body>
+
+ <p><strong>SIFTS Mapping</strong></p>
+
+ <p>
+ SIFTS (Structure integration with function, taxonomy
+ and sequences) provides an up-to-date resource for residue-level
+ mapping between Uniprot and PDB entries. The information is updated and
+ released weekly simultaneously with the release of new PDB entries.
+ SIFTS Entries are published as XML files and made publicly available via an FTP
+ site hosted at the European Bioinformatics Institute.
+ </p>
+
+ <p>
+ At the point of viewing a PDB structure, Jalview downloads a SIFTS file
+ for the target entry and uses it to accurately map the sequence residues with the
+ structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch
+ Alignment algorithm to map sequence residues to structure residues, and that may not
+ always result to a correct mapping since it is computational determined.
+ </p>
+
+ <p>
+ The default method for 'Sequence ↔ Structure' mapping can be configured
+ in the Structure tab in the <strong>Tools → Preferences</strong> dialog box. When 'SIFTS'
+ is enabled as the default, all mappings between 'Sequence ↔ Structure' is
+ performed via SIFTS provided that there is a valid SIFTS entry for PDB structure. If no
+ valid SIFTS resource is available, then the 'Sequence ↔ Structure' mapping falls
+ back to Needleman and Wunsch Alignment algorithm.
+ </p>
+
+ <p>To verify the mapping method used, you can view the mapping output via the structure viewer menu <strong>File → View mapping.</strong> A sample mapping output can be seen in the screenshot below. The highlighted position shows the method used. </p>
+ <p>
+ <img src="sifts_mapping_output.png" align="left" alt="SIFTS mapping output" />
+ </p>
+
+ <p><em>SIFTS Mapping integration was added in Jalview 2.9.1</em></p>
+
+</body>
+</html>
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