5 <title>SIFTS Mapping</title>
9 <p><strong>SIFTS Mapping</strong></p>
12 SIFTS (Structure Integration with Function, Taxonomy
13 and Sequences) provides an up-to-date resource for residue-level
14 mapping between Uniprot and PDB entries. The information is updated and
15 released weekly simultaneously with the release of new PDB entries.
16 SIFTS Entries are published as XML files and made publicly available via an FTP
17 site hosted at the European Bioinformatics Institute.
21 At the point of viewing a PDB structure, if the default mapping method is set as 'SIFTS',
22 Jalview will download a SIFTS file
23 for the target entry and uses it to accurately map the sequence residues with the
24 structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch
25 Alignment algorithm to map sequence residues to structure residues, and that may not
26 always result to a correct mapping since it is computational determined.
30 <strong>Configuration</strong><br/>
31 The default mapping method can be configured via <strong>Tools → Preferences →
32 Structure tab</strong> Then scroll to the 'Sequence ↔ Structure method' section of
33 the dialog box and change the default method. When 'SIFTS' is enabled as the default, all
34 mappings between 'Sequence ↔ Structure' is performed via SIFTS provided that there
35 is a valid SIFTS resource for the PDB entry. If no valid SIFTS resource is available, then
36 the 'Sequence ↔ Structure' mapping falls back to Needleman and Wunsch Alignment algorithm.
39 <p><strong>Multi-Chain Mappings</strong>
40 <br/>One of the main merits of SIFTS is the ability to accurately achieve multi-chain mapping
41 (one-to-many) between a single Uniprot sequence and its corresponding multiple chains in
42 PDB. Consequently, mousing over the uniprot sequence in the alignment window results
43 to highlighting multiple corresponding positions in the structure viewer for the mapped chains.
46 To see this in action, load uniprot sequence for FER1_MAIZE then veiw PDB structure for 3B2F, you
47 will notice that mousing over the sequence results to two positions being highlighted in the
48 structure, also colouring the sequence transfers the color to all the mapped chains in the structure.
52 <Strong>Viewing Mapping Output</Strong> <br/>
53 The mapping output is accessible via <strong>File → View mapping</strong> menu of the structure
54 viewers. The screenshot below is the mapping output for the <Strong>{FER1_MAIZE ↔ 3B2F}</Strong>
55 example described above. Observe that all the two chains were mapped. The mapping method used can be
56 seen within the area highlighted with red boarder. This is useful for visually ascertaining the
57 mapping method when in doubt.
60  <img src="sifts_mapping_output.png" align="left" alt="SIFTS mapping output" />
63 <p><em>SIFTS Mapping integration was added in Jalview 2.9.1</em></p>