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

Client-side interface to obtain data for paralogous genes

Description

Given a KEGG gene id, the function queries the KEGG Sequence Similarity Database (SSDB) for genes that are paralogous to the target gene. Paralogous genes result from duplication of existing genes and then function divergence

Usage

get.paralogs.by.gene(genes.id, start, max.results)

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)
start start an integer to indicate the location of the entry in the query results from which the results will be extracted and returned
max.results max.results an integer to indicate the maximum number of entries that will be extracted from the query results and returned

Details

A given gene may have several paralogous genes. A query to SSDB may have a list of genes that are paralogous to the target gene. start and max.results indicate where on the list to start and stop to extract data and return the results.

Value

The function returns a list of lists. Each sub-list contains data for a gene that is paralogous to the target gene with the following elements:

genes_id1 a character string for the id of the target gene used to query for hologous genes
genes_id2 a character string for the id of the homologous gene found in another organism
sw_score an integer for Smith-Waterman score between genes_id1 and genes_id2
bit_score a numeric value for the bit score between genes_id1 and genes_id2
identity a numeric value between 0 and 1 for the degree of identity between genes_id1 and genes_id2
overlap an integer for the overlapping length between genes_id1 and genes_id2
start_position1 an integer for the start position of the alignment in genes_id1
end_position1 an integer for the end position of the alignment in genes_id1
start_position2 an integer for the start position of the alignment in genes_id2
end_position2 an integer for the end position of the alignment in genes_id2
best_flag_1to2 a boolean that is TRUE if genes_id2 is the best neighbor gene of genes_id1
best_flag_2to1 a boolean that is TRUE if genes_id1 is also the best neighbor gene of genes_id2
definition1 a character string for the definition of genes_id1
definition2 a character string for the definition of genes_id2
length1 an integer for the amino acid length of the genes_id1
length2 an integer for the amino acid length of the genes_id2

Author(s)

Jianhua Zhang

References

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

See Also

get.best.neighbors.by.gene

Examples

    if(require("SSOAP") && require("XML")){
        paraGenes <- get.paralogs.by.gene("eco:b0002", 1, 10)
    }

[Package KEGGSOAP version 1.10.0 Index]