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 


klarakaleb/roma documentation built on April 21, 2024, 8:39 a.m.