Alignments of PDB chains, Rfam seed alignments, and Rfam full sequence families
For each Rfam family that is mapped to a PDB chain, the following files are available;
substitute the desired Rfam family accession id.
- RF00003_combined_seed.fa.gz PDB chains aligned with Rfam seed alignment. PDB chain identifiers and sequences are listed.
- RF00003_combined_seed.sto PDB chain sequences aligned with Rfam seed alignment. PDB chain identifiers are replaced by generic labels for each PDB sequence. Rfam secondary structure should appear at the bottom of the alignment.
- RF00003_15.0_column_to_unit_id.txt Mapping from columns in Rfam seed alignment to unit ids in 3D structures. Columns are numbered starting at 1. You can download the Rfam seed alignment from Rfam. Rfam release is indicated in the filename.
- RF00003_15.0_CCF_column_to_unit_id.txt Mapping from columns in CaCoFold version of the Rfam seed alignment to unit ids in 3D structures. Columns are numbered starting at 1. Rfam release is indicated in the filename.
- RF00003_combined.fa.gz PDB chains aligned to the full Rfam sequence family, with some duplicates removed. More documentation available upon request.
Additional file:
- pdb_chain_to_best_rfam.txt Mapping from PDB chains to their best matching Rfam family, for each sequence range in the PDB chain. A single chain can have more than one match when the matching ranges do not overlap, or overlap up to 10 nucleotides. The last column indicates whether the mapping was made at Rfam or RNA 3D Hub.