seqwalk.design

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

Module Contents

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

  • verbose – bool, True if print and warning statements are desired

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, verbose=True)[source]

design a maximally orthogonal library of N length L sequences

Parameters:

  • N – minimum number of sequences in library

  • L – integer length of desired seqs

  • 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)

  • k_init – initial guess for SSM k value

  • verbose – bool, True if print and warning statements are desired

Returns:

seqs

library of orthogonal sequences

Return type:

list of strings