FoldingSequences

FoldingSequences[sequence,k]⟹sequences

this function takes a sequence and returns a list of subsequences of length k from the entire sequence that could potentially fold.

FoldingSequences[sequence,k,Span[m,n]]⟹sequences

this function takes a sequence and returns a list of subsequences of length k from the position m to positon n in the sequence that could potentially fold.

FoldingSequences[sequence]⟹sequences

this function takes a sequence and returns a list of subsequences from length spesified by the MinLevel option to the largest fold length present from the entire sequence that could potentially fold.

FoldingSequences[sequence,Span[m,n]]⟹sequences

this function takes a sequence and returns a list of subsequences from length spesified by the MinLevel option to the largest fold length present from the position m to positon n in the sequence that could potentially fold.

Details

When spans are provided returns any sequences of length k which inclusively contact the provided region.

Input

Output

General Options

Attributes

Listable

Examples

Basic Examples (2)

Find all 6-mer fold regions:

Find all 4-mer folds the overlap with the given span:

Additional Examples (7)

Find folds at a list of lengths:

Find folds for a list of sequences at a single length:

Find folds for a sequences at a list of span locations:

Given list of spans:

Given list of spans for RNA sequence:

List of lengths and spans:

List of lengths and spans for RNA sequence:

Options (4)

Consolidate (1)

If no length 'k' is provided counts only the largest occurance of a subsequence (e.g. if a folding subsequence of length 6 exists, and consolidate is true, does not return the composite 5,4,3,2,1-mer folds that exist entirely within the 6mer fold):

Degeneracy (1)

Can turn on degeneracy:

MinLevel (1)

Find all folds at least 2 bases in length:

Polymer (1)

Can specify polymer type:

Attributes (1)

Listable (1)

Function is listable: