Sequence Analysis with OmaDB

In OmaDB: R wrapper for the OMA REST API

Another useful function of the OmaDB package is its functionality to exactly and partially match sequences. We will explore this further in this vignette.

Let's say we have a sequence of interest that we want to map, in this case:

 sequence = "MNDPSLLGYPNVGPQQQQQQQQQQHAGLLGKGTPNALQQQLHMNQLTGIPPPGLMNNSDVHTSSNNNSRQLLDQLANGNANMLNMNMDNNNNNNNNNNNNNNNGGGSGVMMNASTAAVNSIGMVPTVGTPVNINVNASNPLLHPHLDDPSLLNNPIWKLQLHLAAVSAQSLGQPNIYARQNAMKKYLATQQAQQAQQQAQQQAQQQVPGPFGPGPQAAPPALQPTDFQQSHIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHER"

We can pass it to the mapSequence() function which returns a list of targets. From this list we can then construct protein objects for which we can obtain further infromation - such as its oma group or its domains. The example response object, generated via mapSequence(sequence), is below.

library(OmaDB)

load('../data/sequence_map.rda')

getObjectAttributes(sequence_map)

targets = getAttribute(sequence_map,'targets')

length(targets) 

protein = targets[[1]][['entry_url']]

One can also directly obtain GO annotations for a given query sequence (protein$ogene_ontology), which results in an object as below:

load('../data/sequence_annotation.rda')

sequence_annotation 

OmaDB documentation built on Nov. 13, 2020, 2 a.m.