gquad {gquad} | R Documentation |
Predicting G quadruplexes
Description
This function predicts G quadruplexes
in ‘x’ (nucleotide sequence(s)).
Nucleotide sequence can be provided in raw or fasta format or as GenBank accession number(s).
Internet is needed to connect to GenBank database, if accession number(s) is given as argument.
Usage
gquad(x, xformat = "default")
Arguments
x |
nucleotide sequence(s) in raw format or a fasta file or a GenBank accession number(s); from which G quadruplexes will be predicted. |
xformat |
a character string specifying the format of x : default (raw), fasta, GenBank (GenBank accession number(s)). |
Details
This function predicts G quadruplexes in nucleic (both DNA and RNA) sequences and provide the position, sequence and length of the predicted motif(s). If any motif is predicted, the degree of likeliness for the motif to be formed is computed and scored as ** (more likely) or as * (less likely).
Value
A dataframe of G quadruplexes’ position, sequence, length and likeliness. If more than one nucleotide sequence is provided as argument, an input ID is returned for motif(s) predicted from each input sequence.
Author(s)
Hannah O. Ajoge
References
paper under review
See Also
gquadO
Examples
## Predicting G quadruplexes from raw nucleotide sequences E1 <- c("TCTTGGGCATCTGGAGGCCGGAAT", "taggtgctgggaggtagagacaggatatcct") gquad(E1) ## Predicting G quadruplexes from nucleotide sequences in fasta file ## Not run: gquad(x="Example.fasta", xformat = "fasta") ## Predicting G quadruplexes from nucleotide sequences, ## using GenBank accession numbers. ## Internet connectivity is needed for this to work. ## Not run: gquad(c("BH114913", "AY611035"), xformat = "GenBank")
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