SIFTS Mapping

From 68cd75cd1fea4f2c184ab031286f4ef0e9fd5f2e Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 5 Sep 2016 17:17:37 +0100 Subject: [PATCH] JAL-2089 reworked and formatted doc for JAL-1479 - SIFTS --- help/html/features/seqmappings.html | 5 +- help/html/features/siftsmapping.html | 102 ++++++++++++++++++---------------- 2 files changed, 56 insertions(+), 51 deletions(-) diff --git a/help/html/features/seqmappings.html b/help/html/features/seqmappings.html index d868cc5..b88aefc 100644 --- a/help/html/features/seqmappings.html +++ b/help/html/features/seqmappings.html @@ -25,7 +25,7 @@

Mapping Between Different Sequences -

A new feature in Jalview 2.3 is the ability to map between sequences in different domains, based on alignment, or by the use of explicit mappings provided by databases.

@@ -43,6 +43,7 @@ allows sequence features to be mapped directly from UniProt das sources to their coding region on EMBL sequence records.

In Jalview 2.9.1 SIFTS Mapping was added as a better means for explicitly identifying the coordinates corresponding to a displayed sequence when viewing a PDB structure associated with a sequence

+ SIFTS Mapping between PDB and + UniProt data was introduced in Jalview 2.10 diff --git a/help/html/features/siftsmapping.html b/help/html/features/siftsmapping.html index 08089ad..80c0294 100644 --- a/help/html/features/siftsmapping.html +++ b/help/html/features/siftsmapping.html @@ -2,65 +2,69 @@ -SIFTS Mapping +SIFTS Mapping from UniProt for PDB Structures - -

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.

- +

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 its built-in Needleman and Wunsch + global alignment algorithm. This method of mapping was used for all + structures prior to version 2.10.

- 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. + 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, since the biological unit will 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, 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.

- 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
The mapping provided + by the SIFTS record 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, and confirms that all two chains + were mapped. The mapping method used can be seen within the area + highlighted with red boarder.

- 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. + + SIFTS mapping output

- - SIFTS mapping output - - -

SIFTS Mapping integration was added in Jalview 2.9.1

- + SIFTS Mapping integration was added in Jalview 2.10 +

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