get.motifs.by.gene {KEGGSOAP}R Documentation

Client-side interface to obtain the name of genes that are homologous to a given gene

Description

This function queries the Pfam, TIGRFAM, PROSITE pattern, and/or PROSITE profile databases for the motifs of a given gene. A motif is a locally conserved region of a sequence or a short sequence pattern shared by a set of sequences

Usage

get.motifs.by.gene(genes.id, db)

Arguments

genes.id genes.id a character string for the id used by KEGG to represent the gene of interest. The id normally consists of three letters followed by a colon and then several numbers. The three letters are from the first letter of the genus name and the first two letters of the species name of the scientific name of the organism of concern (e. g. hsa:111 for Homo Sapiens)
db db a character string for the name of the data to search for motifs. Valid database names include pfam, tfam, pspt, pspf for the Pfam, TIGRFAM, PROSITE pattern, and PROSITE profile, respectively, or all for all the four databases

Details

The motif ids obtained can be used to search for the genes that contain the motif across organism using get.genes.by.motifs

Value

The function returns a list of lists with each of the sub-list having the following elements:

motif_id a character string for the id of the motif found
definition a character string for the definition of the motif
genes_id a character string for the KEGG genes_id of the gene that contains the motif and used to search the database(s)
start_position an integer for the start position of the motif match
end.position an integer for the end position of the motif match
score a numeric value for the score of the motif match for TIGRFAM and PROSITE databases
evalue a numeric value for the E-value of the motif match for Pfam database

Author(s)

Jianhua Zhang

References

http://www.genome.jp/kegg/soap/doc/keggapi_manual.html

See Also

get.genes.by.motifs

Examples

    if(require("SSOAP") && require("XML")){
        motifs <- get.motifs.by.gene("eco:b0002", "pfam")
        sapply(motifs, function(x) x$motif_id)
    } 

[Package KEGGSOAP version 1.4.0 Index]