SIFTS

The SIFTS module of MIToS allows to obtain the residue-level mapping between databases stored in the SIFTS XML files. It makes easy to assign PDB residues to UniProt/Pfam positions. Given the fact that pairwise alignments can lead to misleading association between residues in both sequences, SIFTS offers more reliable association between sequence and structure residue numbers.

Features

• Download and parse SIFTS XML files
• Store residue-level mapping in Julia
• Easy generation of OrderedDicts between residues numbers

using MIToS.SIFTS

A SIFTSResidue object stores the SIFTS residue level mapping for a residue. It has the following fields that you can access at any moment for query purposes:

- `PDBe` : A `dbPDBe` object, it's present in all the `SIFTSResidue`s.
- `UniProt` : A `dbUniProt` object or `missing`.
- `Pfam` : A `dbPfam` object or `missing`.
- `NCBI` : A `dbNCBI` object or `missing`.
- `InterPro` : An array of `dbInterPro` objects.
- `PDB` : A `dbPDB` object or `missing`.
- `SCOP` : A `dbSCOP` object or `missing`.
- `SCOP2` : An array of `dbSCOP2` objects.
- `SCOP2B` : A `dbSCOP2B` object or `missing`.
- `CATH` : A `dbCATH` object or `missing`.
- `Ensembl` : An array of `dbEnsembl` objects.
- `missing` : It's `true` if the residue is missing, i.e. not observed, in the structure.
- `sscode` : A string with the secondary structure code of the residue.
- `ssname` : A string with the secondary structure name of the residue.

dbCATH stores the residue id, number, name and chain in CATH as strings.

dbEnsembl stores the residue (gene) accession id, the transcript, translation and exon ids in Ensembl as strings, together with the residue number and name using the UniProt coordinates.

dbInterPro stores the residue id, number, name and evidence in InterPro as strings.

dbNCBI stores the residue id, number and name in NCBI as strings.

dbPDB stores the residue id, number, name and chain in PDB as strings.

dbPDBe stores the residue number and name in PDBe as strings.

dbPfam stores the residue id, number and name in Pfam as strings.

dbSCOP stores the residue id, number, name and chain in SCOP as strings.

dbSCOP2 stores the residue id, number, name and chain in SCOP2 as strings.

dbSCOP2B stores the residue id, number, name and chain in SCOP2B as strings. SCOP2B is expansion of SCOP2 domain annotations at superfamily level to every PDB with same UniProt accession having at least 80% SCOP2 domain coverage.

dbUniProt stores the residue id, number and name in UniProt as strings.

parse(document::LightXML.XMLDocument, ::Type{SIFTSXML}; chain=All, missings::Bool=true)

Returns a Vector{SIFTSResidue} parsed from a SIFTSXML file. By default, parses all the chains and includes missing residues.

downloadsifts(pdbcode::String; filename::String, source::String="https")

Download the gzipped SIFTS XML file for the provided pdbcode. The downloaded file will have the default extension .xml.gz. While you can change the filename, it must include the .xml.gz ending. The source keyword argument is set to "https" by default. Alternatively, you can choose "ftp" as the source, which will retrieve the file from the EBI FTP server at ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/. However, please note that using "https" is highly recommended. This option will download the file from the EBI PDBe server at https://www.ebi.ac.uk/pdbe/files/sifts/.

Parses a SIFTS XML file and returns a OrderedDict between residue numbers of two DataBases with the given identifiers. A chain could be specified (All by default). If missings is true (default) all the residues are used, even if they haven’t coordinates in the PDB file.