Author: Klara Kaleb
Date: 2026-04-30

# Sequence Analysis with OmaDB

#### Klara Kaleb

#### 2026-04-30

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