annotateSequence: Map GO annotation to a sequence that is not available in the...
In klarakaleb/roma: R wrapper for the OMA REST API
View source: R/annotateSequence.R
annotateSequence R Documentation
Map GO annotation to a sequence that is not available in the OMA Browser
Description
This function obtain Gene Ontology annotation for a given sequence that
does not need to exist in the OMA Browser so far. The query sequence will
analysed and a fast homology detection approach based on kmers will be used
to detect the closest sequences in OMA. GO annotations for these top hits
will be used to annotated the query sequence.
Usage
annotateSequence(query)
Arguments
query
the sequence to be annotated, it can be either a string or an
AAString object from the Biostrings package
Value
a data.frame containing the the GO annotation information of the
most similar protein to the query sequence
Examples
annotateSequence(query='MNDPSLLGYPNVGPQQQQQQQQQQHAGLLGKGTPNALQQQLHMNQLTGIPPPGLMNNSDVHTSSNNNSRQLLDQLANGNANMLNMNMDNNNNNNNNNNNNNNNGGGSGVMMNASTAAVNSIGMVPTVGTPVNINVNASNPLLHPHLDDPSLLNNPIWKLQLHLAAVSAQSLGQPNIYARQNAMKKYLATQQAQQAQQQAQQQAQQQVPGPFGPGPQAAPPALQPTDFQQSHIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHERRFIEINTDGEPQREYDSLQQSTEHLATDLAKRTFTVLSYNTLCQHYATPKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVESKTFEEYWVPLLDKHGYTGIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDFSGAWMKHKKFQRTEDYLNRAMNKDNVALFLKLQHIPSGDTIWAVTTHLHWDPKFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELINTGRVQIHQEGNGRDFGYMSEKNFSHNLALKSSYNCIGELPFTNFTPSFTDVIDYIWFSTHALRVRGLLGEVDPEYVSKFIGFPNDKFPSDHIPLLARFEFMKTNTGSKKV')
klarakaleb/roma documentation built on Jan. 27, 2024, 3:46 p.m.
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View source: R/annotateSequence.R
| annotateSequence | R Documentation |
Map GO annotation to a sequence that is not available in the OMA Browser
Description
This function obtain Gene Ontology annotation for a given sequence that does not need to exist in the OMA Browser so far. The query sequence will analysed and a fast homology detection approach based on kmers will be used to detect the closest sequences in OMA. GO annotations for these top hits will be used to annotated the query sequence.
Usage
annotateSequence(query)
Arguments
query |
the sequence to be annotated, it can be either a string or an AAString object from the Biostrings package |
Value
a data.frame containing the the GO annotation information of the most similar protein to the query sequence
Examples
annotateSequence(query='MNDPSLLGYPNVGPQQQQQQQQQQHAGLLGKGTPNALQQQLHMNQLTGIPPPGLMNNSDVHTSSNNNSRQLLDQLANGNANMLNMNMDNNNNNNNNNNNNNNNGGGSGVMMNASTAAVNSIGMVPTVGTPVNINVNASNPLLHPHLDDPSLLNNPIWKLQLHLAAVSAQSLGQPNIYARQNAMKKYLATQQAQQAQQQAQQQAQQQVPGPFGPGPQAAPPALQPTDFQQSHIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHERRFIEINTDGEPQREYDSLQQSTEHLATDLAKRTFTVLSYNTLCQHYATPKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVESKTFEEYWVPLLDKHGYTGIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDFSGAWMKHKKFQRTEDYLNRAMNKDNVALFLKLQHIPSGDTIWAVTTHLHWDPKFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELINTGRVQIHQEGNGRDFGYMSEKNFSHNLALKSSYNCIGELPFTNFTPSFTDVIDYIWFSTHALRVRGLLGEVDPEYVSKFIGFPNDKFPSDHIPLLARFEFMKTNTGSKKV')
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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