Finds positions of specified sequence patterns in a list of sequences of the same length ordered by a provided index. Sequence patterns can be consensus sequences of variable length and can contain IUPAC ambiguity code. Position of each pattern occurrence is specified in two-dimensional matrix, i.e. the first coordinate provides the ordinal number of the sequence and the second coordinate gives the position within the sequence where the pattern occurs.
Finds positions of sequence motif hits above a specified threshold in a list of sequences of the same length ordered by a provided index. Motif is specified by a position weight matrix (PWM) that contains estimated probability of base b at position i and is usually constructed via call to PWM function. Position of each motif hit is specified in two-dimensional matrix, i.e. the first coordinate provides the ordinal number of the sequence and the second coordinate gives the position within the sequence where the motif occurs.
Provides motif scanning scores along the full length of a sequence for a list of sequences of the same length ordered by a provided index. Motif is specified by a position weight matrix (PWM) that contains estimated probability of base b at position i and is usually constructed via call to PWM function. Scanning scores are returned in the form of a two-dimensional matrix, where the rows are sequences ordered by the specified index and the columns are relative positions within the sequence. Each cell in the matrix contains the score of the specified motif in the given sequence starting at the given position. The resulting matrix can be used to visualise motif occurrences and their strength in an ordered set of sequences centered at a common reference point.
Plots density of motif occurrences in an ordered set of sequences of the same length in the form of a two dimensional map centered at a common reference position. Motif is specified by a position weight matrix (PWM) that contains estimated probability of base b at position i, and only motif hits above specified threshold are taken into account and plotted.
Plots average profile of motif occurrence for a set of input sequences of the same length. Motif is specified by a position weight matrix (PWM) that contains estimated probability of base b at position i, and only motif hits above specified threshold are taken into account.
Plots heatmap of motif scanning scores for a set of sorted sequences of the same length in the form of a two dimensional map centered at a common reference position. Motif is specified by a position weight matrix (PWM) that contains estimated probability of base b at position i, and the percentage of the maximal PWM score is plotted for each position (nucleotide) in each sequence.
Plots density of sequence pattern occurrences in an ordered set of sequences of the same length in the form of a two dimensional map centered at a common reference position. Multiple sequence patterns can be processed at once and one plot per pattern will be created with the same color scale across all plots, allowing visual density comparison across different patterns.
Plots average profile of sequence pattern occurrence for a set of input sequences of the same length. Multiple sequence patterns can be processed at once and visualised in the same plot, allowing comparison across different patterns.
seqPattern-package
(Package: seqPattern) :
Visualising oligonucleotide patterns and motif occurences across a set
Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.
providing 
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