canprot (version 0.1.2)

canprot: Amino Acid Compositions of Human Proteins

Description

Data for amino acid compositions, and updates to UniProt IDs.

Format

The columns of human_aa are compatible with the layout used for amino acid compositions in CHNOSZ (see thermo):

protein	character	Identification of protein
organism	character	Identification of organism
ref	character	Reference key for source of compositional data
abbrv	character	Abbreviation or other ID for protein
chains	numeric	Number of polypeptide chains in the protein

Here, the protein column contains the UniProt ID (accession), possibly with a suffix indicating the isoform of the protein (esp. from human_additional.csv).

Details

These amino acid compositions were compiled from amino acid sequences downloaded from UniProt. Amino acid sequences of human proteins were obtained from files in the UniProt reference proteome, dated 2016-04-03, downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/.

The amino acid compositions of human proteins are stored in three files. human_base.Rdata contains amino acid compositions of proteins in the UniProt reference proteome (UP000005640_9606.fasta.gz containing canonical, manually reviewed sequences). human_additional.Rdata contains amino acid compositions of additional proteins in the UniProt reference proteome (UP000005640_9606_additional.fasta.gz containing isoforms and unreviewed sequences). human_extra.csv contains amino acid compositions of other (“extra”) proteins identified in proteomic experiments but not listed in one of the files above.

On loading the package, the individual data files are read and combined using rbind, and the result is assigned to the human_aa object in the canprot environment.

As an aid for processing some datasets that use old (obsoleted) UniProt IDs, the corresponding new (current) IDs are are stored in uniprot_updates. uniprot_updates also lists the source (i.e. reference key) that uses each old ID.

Examples

# NOT RUN {
nrow(get("human_aa", canprot))
# }