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, if the default mapping method is set as 'SIFTS', - Jalview will download 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.
- Configuration
- The default mapping method can be configured via Tools → Preferences →
- Structure tab Then scroll to the 'Sequence ↔ Structure method' section of
- the dialog box and change the default method. When 'SIFTS' is enabled as the default, all
- mappings between 'Sequence ↔ Structure' is performed via SIFTS provided that there
- is a valid SIFTS resource for the PDB entry. If no valid SIFTS resource is available, then
- the 'Sequence ↔ Structure' mapping falls back to Needleman and Wunsch Alignment algorithm.
-
Multi-Chain Mappings
-
One of the main merits of SIFTS is the ability to accurately achieve multi-chain mapping
- (one-to-many) between a single Uniprot sequence and its corresponding multiple chains in
- PDB. Consequently, mousing over the uniprot sequence in the alignment window results
- to highlighting multiple corresponding positions in the structure viewer for the mapped chains.
+ 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 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.
+- To see this in action, load uniprot sequence for FER1_MAIZE then veiw PDB structure for 3B2F, you - will notice that mousing over the sequence results to two positions being highlighted in the - structure, also colouring the sequence transfers the color to all the mapped chains in the structure. -
- + Viewing Mapping Output
- Viewing Mapping Output
- The mapping output is accessible via File → View mapping menu of the structure
- viewers. The screenshot below is the mapping output for the {FER1_MAIZE ↔ 3B2F}
- example described above. Observe that all the two chains were mapped. The mapping method used can be
- seen within the area highlighted with red boarder. This is useful for visually ascertaining the
- mapping method when in doubt.
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SIFTS Mapping integration was added in Jalview 2.9.1
- + SIFTS Mapping integration was added in Jalview 2.10 + + \ No newline at end of file