True > # x > y (x is neoschizomer of y) > Acc65I > Acc65I # same enzyme => False False > Acc65I > Asp718I # same site, same cut => False False > Acc65I > EcoRI # different site => False False > Acc65I > KpnI # same site, different cut => True True > # x % y (fragments produced by x and fragments produced by y > # can be directly ligated to each other) > Acc65I % Asp718I > # Here are the results of the 4 operators > # for each pair of enzymes: > # x = y (x is y) > Acc65I = Acc65I # same enzyme => True True > Acc65I = KpnI # all other cases => False False > Acc65I = Asp718Iįalse > # x != y (x and y are not true isoschizomers) > Acc65I != Acc65I # same enzyme => False False > Acc65I != Asp718I # different enzymes, but cut same manner => False False > Acc65I != KpnI # all other cases => True True > Acc65I != EcoRI > # KpnI is a neoschizomers of the 2 others. 'G_GTAC^C' > # Asp718I and Acc65I are true isoschizomers, > # they recognise the same site and cut it the > # same way. Let's use Acc65I and its isoschizomers as example: % (test compatibilty) Test the compatibility of the ending produced by the enzymes (will be True if the fragments produced with one of the enzyme can directly be ligated to fragments produced by the other). > (test for neoschizomer) True if the enzymes recognise the same site, but cut it in a different way (i.e. true isoschizomers will not being the same enzymes, are not different since they are interchangeable). Two enzymes are not different if the result produced by one enzyme will always be the same as the result produced by the other (i.e. != (test for different site or cutting) It will return True if the two sides of the operator are different. the only thing which is equal to EcoRI is EcoRI). *Same" is defined as: same name, same site, same overhang (i.e. = (test identity) It will return True if the two sides of the operator are the same. All these operator compares two enzymes together and either return True or False. Restriction enzymes define 4 comparative operators =, !=, > and %. In a circular sequence however, the site is effectively present when the beginning and end of the sequence are joined. This site does not exist in a linear sequence as the EcoRI site is split into two halves at the start and the end of the sequence. > arch(new_seq, linear = False)Īs you can see using linear=False, make a site appearing in the sequence new_seq. > new_seq = Seq( 'TTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA', IUPACAmbiguousDNA()) To import the enzymes, open a Python shell and type: The chapter is constructed as an interactive Python session and the best way to read it is with a Python shell open alongside you. This chapter will lead you through a quick overview of the facilities offered by the Restriction package of Biopython. Restriction make use of the facilities offered by REBASE and contains classes for more than 800 restriction enzymes. This package will allow you to work with restriction enzymes and realise restriction analysis on your sequence. The restriction enzyme package is situated in Bio.Restriction. Annexe: modifying dir() to use with from Bio.Restriction import *.Restriction reports cutting sites not enzyme recognition sites.Sites found at the edge of linear DNA might not be accessible in a real digestion.Non standard bases in DNA are not allowed.Compiling a new dictionary with ranacompiler.py.Fetching the recent enzyme files with rebase_update.py.Fetching the recent enzyme files manually from Rebase.Using / and // operators with FormattedSeq.Unlike Bio.Seq, FormattedSeq retains information about their shape.Advanced features: the FormattedSeq class.The Analysis class: even simpler restriction analysis.AllEnzymes and CommOnly: two preconfigured RestrictionBatches.Analysing sequences with a RestrictionBatch.Removing enzymes from a RestrictionBatch.Restricting a RestrictionBatch to a particular supplier.The RestrictionBatch class: a class to deal with several enzymes.
Other facilities provided by the enzyme classes.Retrieving the sequences produced by a digestion.Working with restriction enzymes Table of contents
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