`seqwalk.design`

Module Contents

Functions

`max_size`(L, k[, alphabet, RCfree, GClims, ...])	design a max size library of length L sequences with SSM k
`max_orthogonality`(N, L[, alphabet, RCfree, GClims, ...])	design a maximally orthogonal library of N length L sequences

seqwalk.design.max_size(L, k, alphabet='ACT', RCfree=False, GClims=None, prevented_patterns=['AAAA', 'CCCC', 'GGGG', 'TTTT'])[source]

design a max size library of length L sequences with SSM k

Parameters:

L – integer length of desired seqs
k – SSM k value
alphabet – string of allowable letters (default “ACT”)
RCfree – bool, True if orthogonality with RCs is required
GClims – tuple of (GCmin, GCmax), allowable range of number of GC bases
prevented_patterns – list of prevented patterns (default 4N)

Returns:

seqs: library of orthogonal sequences

Return type:

list of strings

seqwalk.design.max_orthogonality(N, L, alphabet='ACT', RCfree=False, GClims=None, prevented_patterns=['AAAA', 'CCCC', 'GGGG', 'TTTT'], k_init=None)[source]

design a maximally orthogonal library of N length L sequences