diopt: Query DIOPT database

In oganm/homologene: Quick Access to Homologene and Gene Annotation Updates

Query DIOPT database

Description

Query DIOPT database (https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl) for orthologues. DIOPT database uses multiple tools to find gene orthologues. Sadly they don't have an API so this function queries by visiting the site and filling up the form. By default each query will take a minimum of 10 seconds due to delay parameter. This is taken from their robots.txt at the time this function is written. Note that DIOPT is not necesariy in sync with homologene database as provided in this package.

Usage

diopt(genes, inTax, outTax, delay = 10)

Arguments

genes	A vector of gene identifiers. Anything that DIOPT accepts
inTax	taxid of the species that the input genes are coming from
outTax	taxid of the species that you are seeking homology. 0 to query all species.
delay	How many seconds of delay should be between queries. Default is 10 based on the robots.txt at the time this function is written.

Details

DIOPT does not support all species available in the homologene database. The supported species are:

4896

Schizosaccharomyces pombe

4932

Saccharomyces cerevisiae

6239

Caenorhabditis elegans

7227

Drosophila melanogaster

7955

Danio rerio

8364

Xenopus (Silurana) tropicalis

9606

Homo sapiens

10090

Mus musculus

10116

Rattus norvegicus

3702

Arabidopsis thaliana

Value

A data frame

oganm/homologene documentation built on Nov. 5, 2023, 8:39 a.m.