annotateSequence: Map GO annotation to a sequence that is not available in the...

View source: R/annotateSequence.R

annotateSequenceR 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/OmaDB documentation built on April 18, 2024, 8:03 a.m.