schemarecomb.parent_alignment

Alignment of parental sequences for protein recombination.

This module provides the definition of schemarecomb.ParentSequences, which represents an alignment of parental protein sequences used in schemarecomb library creation. The module can be used directly to use accessory functions for calculating identity between sequences, querying the BLAST web interface, or selecting additional parent sequences from a list of candidates.

Functions

calc_identity(sr1, sr2)

Calculate the BLAST identity between two sequences.

choose_candidates(candidate_sequences, …)

Choose the ideal set of candidate sequences.

local_muscle(records)

Align sequences with MUSCLE and set to aligned_sequences.

query_blast(query_seq[, database, maximum_hits])

Gets sequences from query_seq BLAST hits.

web_muscle(records)

Align sequences using MUSCLE on EMBL-EBI Web Services.