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Crecombio

A simple Cre, Flp and other site-specific recombination simulator.

Background

Site-specific recombinase proteins rearrange one or two DNA molecules, through recombination at certain recognized sequences. In Flp-FRT recombination, a tyrosine family member recombinase protein, flippase, recognizes FRT (flippase recognition target) sites and performs inversion, excision, insertion or translocation of DNA in a reversible manner, depending on the configuration of the FRT sites. Another, directional, system utilizes serine integrases to catalyze rearrangements at DNA sequences called attachment (att) sites.

Site-specific recombinations can be categorised in many ways:

  • directionality: reversible or not
  • recombination enzyme used
  • recombination sequence used
  • number of DNA molecules present in the reaction and number of recombination sites in each molecule
  • purpose: inversion, excision, insertion and translocation

For simulating homologous recombination and other assemblies, use DNA Cauldron and EGF CUBA Simulate Golden Gate Assemblies / Simulate multi-method assemblies.

Crecombio is currently intended for simple 1- or 2-molecule recombination simulations. For more complicated procedures, such as the serine integrase recombinational assembly (SIRA), described in Merrick et al. (Serine Integrases: Advancing Synthetic Biology. ACS Synth. Biol. 2018, 7, 299−310), use it in an iterative manner. Alternatively DNA Cauldron's classes can be used with custom-defined enzymes to simulate the cleavage and recombination.

Work in progress: - Simulating att recombinations - Searching nonspecific (ambiguous) sites - Handling circular sequences - Summary of simulation in a PDF report

Flp/FRT recombination

Usage

from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
import crecombio
excision_seq = SeqRecord(Seq("GACTGATGTGACGTGTGACAGCTGACGAAGTTCCTATTCtctagaaaGtATAGGAACTTCAAAAAAAAAAAAAAAAAAAAAAGAAGTTCCTATTCtctagaaaGtATAGGAACTTCCCCCCCCCCCCCCCCCCCCCCCCCCCC".upper()))
results = crecombio.recombine([excision_seq])
print(results[0].seq)
# GACTGATGTGACGTGTGACAGCTGACGAAGTTCCTATTCTCTAGAAAGTATAGGAACTTCCCCCCCCCCCCCCCCCCCCCCCCCCCC

inversion_seq = SeqRecord(Seq("GACTGATGTGACGTGTGACAGCTGACGAAGTTCCTATTCtctagaaaGtATAGGAACTTCAAAAAAAAAAAAAGGGGGGGGGGGGGAAGTTCCTATaCtttctagaGAATAGGAACTTCCCCCCCCCCCCCCCCCCCCCCCCCCCC".upper()))
results = crecombio.recombine([inversion_seq])
print(results[0].seq)
# GACTGATGTGACGTGTGACAGCTGACGAAGTTCCTATTCTCTAGAAAGTATAGGAACTTCCCCCCCCCCCCCTTTTTTTTTTTTTGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCCCCCCCCCCCCCCCCCCCCCCCCCCCC

See the examples folder for two-sequence recombination examples.

License = MIT

Crecombio is free software, which means the users have the freedom to run, copy, distribute, study, change and improve the software.

Crecombio was written at the Edinburgh Genome Foundry by Peter Vegh and is released under the MIT license.