skbio.alignment.local_pairwise_align_protein¶
- skbio.alignment.local_pairwise_align_protein(seq1, seq2, gap_open_penalty=11, gap_extend_penalty=1, substitution_matrix=None)[source]¶
Locally align exactly two protein seqs with Smith-Waterman
State: Experimental as of 0.4.0.
- Parameters:
seq1 (Protein) – The first unaligned sequence.
seq2 (Protein) – The second unaligned sequence.
gap_open_penalty (int or float, optional) – Penalty for opening a gap (this is substracted from previous best alignment score, so is typically positive).
gap_extend_penalty (int or float, optional) – Penalty for extending a gap (this is substracted from previous best alignment score, so is typically positive).
substitution_matrix (2D dict (or similar), optional) – Lookup for substitution scores (these values are added to the previous best alignment score); default is BLOSUM 50.
- Returns:
TabularMSA
object containing the aligned sequences, alignment score (float), and start/end positions of each input sequence (iterable of two-item tuples). Note that start/end positions are indexes into the unaligned sequences.- Return type:
See also
local_pairwise_align
,local_pairwise_align_nucleotide
,skbio.alignment.local_pairwise_align_ssw
,global_pairwise_align
,global_pairwise_align_protein
,global_pairwise_align_nucelotide
Notes
Default
gap_open_penalty
andgap_extend_penalty
parameters are derived from the NCBI BLAST Server [1].The BLOSUM (blocks substitution matrices) amino acid substitution matrices were originally defined in [2].
References