+ SIFTS Mapping
- +
- 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.
+ SIFTS Mapping for UniProt sequences and PDB
+ Structures
SIFTS (Structure Integration with Function,
+ Taxonomy and Sequences) is a database of residue-level mappings
+ between UniProt protein sequences, and protein structures found in
+ the PDB. The database is updated for each PDB release, and is
+ provided by the PDBe
+ at EMBL-EBI.
- 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. +
When Jalview imports PDB data for a protein sequence found in + UniProt, either via the 'View 3D Structure...' option, or the 'Fetch + DB Refs' web services menu, Jalview will also download its SIFTS + record and use that information to construct a mapping between the + sequence and downloaded structure.
+If, for some reason, no SIFTS mapping data exists, then Jalview + will generate a mapping using the built-in Needleman and Wunsch + global alignment algorithm. This is how sequence-structure mappings + were created before version 2.10.
+Controlling and troubleshooting SIFTS mappings
+ Configuration options controlling whether SIFTS mappings are used
+ can be found in the Tools → Preferences →
+ Structure tab, under 'Sequence ↔ Structure method'.
Note:
+ Changing the configuration will only affect how new mappings are
+ created. In order to recompute mappings for structures already
+ loaded, please reload the sequence & structural data.
- The default method for 'Sequence ↔ Structure' mapping can be configured
- in the Structure tab in the Tools → Preferences 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.
+ Multi-Chain Mappings
SIFTS gives Jalview the
+ ability to display multi-chain mappings between UniProt sequences
+ and PDB structure data. This is important when working with
+ multimeric proteins, when the biological assembly can contain several
+ structures for the same protein sequence. Multi-chain mapping allows
+ all residues in a structure to be located in the alignment, and
+ also, when shading the structure by sequence colours, enables
+ conservation patterns between oligomer interfaces to be explored.
To verify the mapping method used, you can view the mapping output via the structure viewer menu File → View mapping. A sample mapping output can be seen in the screenshot below. The highlighted position shows the method used.
+To see this in action, Retrieve the UniProt sequence + FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over + the sequence results to two positions being highlighted in the + structure, and colouring the alignment transfers the color to all + the mapped chains in the structure.
+ +
+ Viewing Mapping Output
The mapping provided
+ by the SIFTS record is accessible via File →
+ View mapping menu of the structure viewers. The screenshot below
+ shows the mapping created between UniProt sequence FER1_MAIZE and proteins in PDB 3B2F, which reports thattwo chains
+ were mapped. The mapping method is also reported (highlighted with red border).
+
+
+
+
-
+ SIFTS Mapping integration was added in Jalview 2.10
SIFTS Mapping integration was added in Jalview 2.9.1
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