Sequence Analysis with OmaDB

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)

## [1] "query : character"
## [1] "identified_by : character"
## [1] "targets : list"

targets = getAttribute(sequence_map,'targets')

length(targets) 

## [1] 1

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 

##   Qualifier      GO_ID                                With Evidence     Date
## 1           GO:0003677 Approx:DICDI02796:239.3634208239752      IEA 20180102
## 2           GO:0005509 Approx:DICDI02796:239.3634208239752      IEA 20180102
## 3           GO:0005634 Approx:DICDI02796:239.3634208239752      IEA 20180102
## 4           GO:0006351 Approx:DICDI02796:239.3634208239752      IEA 20180102
## 5           GO:0006355 Approx:DICDI02796:239.3634208239752      IEA 20180102
## 6           GO:0007275 Approx:DICDI02796:239.3634208239752      IEA 20180102
##   DB_Object_Type DB_Object_Name Aspect Assigned_By
## 1        protein                     F OMA_FastMap
## 2        protein                     F OMA_FastMap
## 3        protein                     C OMA_FastMap
## 4        protein                     P OMA_FastMap
## 5        protein                     P OMA_FastMap
## 6        protein                     P OMA_FastMap
##                                      GO_name          DB DB.Reference Synonym
## 1                                DNA binding OMA_FastMap  OMA_Fun:002        
## 2                        calcium ion binding OMA_FastMap  OMA_Fun:002        
## 3                                    nucleus OMA_FastMap  OMA_Fun:002        
## 4               transcription, DNA-templated OMA_FastMap  OMA_Fun:002        
## 5 regulation of transcription, DNA-templated OMA_FastMap  OMA_Fun:002        
## 6         multicellular organism development OMA_FastMap  OMA_Fun:002