bioseq.patterns

require(GCModeller); #' Tools for sequence patterns imports "bioseq.patterns" from "seqtoolkit";

Tools for sequence patterns

.NET clr type export
motif_match: MotifMatch	motif model sequence site matches result

.NET clr function exports
as.data.frame.sequencegraph	SequenceGraph: A machine learning vector model for motif analysis
as.data.frame.msamotif	MSAMotif:
as.data.frame.motifmatch	MotifMatch: motif model sequence site matches result
plot.object	any kind:
open.seedFile	open the sequence seed scan data file
pull.all_seeds	pull all of the sequence seed data from the given seed scan data file
read.meme_xml	read the xml motif data model output from the meme program
toPWM	convert the meme document to motif PWM model object
gibbs_scan	make a motif scan from the given sequence collection
view.sites	display the motif match sites on the given target sequence
read.motifs	read sequence motif json file.
read.scans	read the motif match scan result table file
top_sites	takes the top motif match sites by a set of the given filter threshold values
as.seq_graph	make the sequence graph embedding data of the given sequence collection
motif.find_sites	find the target loci match sites of the given sequence data based on the motif PWM model
palindrome.mirror	Search mirror palindrome sites for a given seed sequence
seeds	create all of the possible seed sequence fragments of the given alphabet base letters
motifString	convert the given sequence motif object as a regexp liked format pattern string for do motif matches
create.seeds	create the sequence seeds data from the given fasta sequence collection, and then save the generated seed data into the target seed data file
find_motifs	find possible motifs of the given sequence collection
plot.seqLogo	Drawing the sequence logo just simply modelling this motif site from the clustal multiple sequence alignment.
scaffold.orthogonality	analyses orthogonality of two DNA-Origami scaffold strands. Multiple criteria For orthogonality Of the two sequences can be specified to determine the level of orthogonality.
split_match_source	split the motif matches result in parts by its gene source

[Document Index]