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Genome View

Overview

The Genome View provides graphical summaries of the correspondences between PDB Entity sequences and genomes. Protein and genome alignments are loaded from the RCSB PDB 1D Coordinate Server. This resource integrates alignments from multiple resources and databases including UniProtKB, RefSeq and SIFTS.
This view will display what regions of the different gene products are covered by the PDB Entity and will allow to explore the relationships between residue indexes and their corresponding nucleotide coordinates at genome level.

Documentation

This feature is available from the Genome View tab on the Structure Summary Page. For example, clicking on the Genome Tab for a PDB entry (e.g. 5IIT) the mapping of the protein sequence of the protein entities (UniProtKB and NCBI RefSeq) is displayed at genome level.
For each mapping the following conventions are used:

How-To

  1. In order to explore the protein-genome mapping click on the Genome Tab of the Structure Summary Page (e.g. 5IIT)
  2. In this page a drop down menu will allow selection of the entity to explore. Only those entities that could be mapped to a reference genome will be available
  3. A particular Entity may be composed of different protein fragments and thus, it may map to multiple chromosomes, the second drop down menu will allow to explore the different chromosomes
  4. Commonly a chromosome ideogram will be displayed and the Entity position will be indicated with a red triangle

Responsive and Interactive Properties


For Advanced Users

Genome / Structure alignments API is available at 1D Coordinate Server