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Finding Motifs: IUPAC and RegEx, an Overview

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End of Section 5, moving to Section 6. For anyone also following the book there will be a jump at the end of chapter 8, so we are not touching the final script that deals with different reading frames here. We are going straight, or almost, to another take of Regular Expressions. We are going to check some aspects of restriction enzymes, but first we are going to touch base with motif finding in DNA sequences. We already saw how to use the re module and to do some simple regular expression searches. Basically our motif search was very simple, with run-time user input using

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motif = re.compile('%s' % inmotif)

where inmotif was the short string sequence entered. Enhancing this a little bit we will first create a more advanced regex search using mismatches in the sequences and after we will see (as in the book) how to translate IUPAC code to regex. The IUPAC table is

A - Adenine 
C - Cytosine 
G - Guanine 
T - Thymine 
U - Uracil 
M - A or C 
R - A or G 
W - A or T 
S - C or G 
Y - C or T 
K - G or T 
V - A or C or G 
H - A or C or T 
D - A or G or T
B - C or G or T 
X - A or C or G or T 
N - A or C or G or T 

You are going to use basic Python to do this. There are mode advanced ways to reach the same goals, but as we haven’t seen a lot of dictionaries it would be great to check them again. The first idea for the table above is to use a dictionary for the codes that represent two or more nucleotides, as dictionary keys would be ideal to include in regex elements. Our basic dictionary would look like this

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iupacdict = {'M':'[AC]', 'R':'[AG]', 'W':'[AT]', 'S':'[CG]', 'Y':'[CT]',
'K':'[GT]', 'V':'[ACG]', 'H':'[ACT]', 'D':'[AGT]', 'B':'[CGT]', 'X':'[ACGT]', 'N':'[ACGT]'}

We include the square brackets around each key because these brackets inside a regex indicate a match in one of the characters. This dictionary would be really advantageous for restriction enzymes too. Now in order to find a motif we need to create a regular expression from the consensus sequence of the motif model, that can be for instance a transcription factor binding site. Let’s say we have a GATA3 model of binding site which has a model NNGATARNG what would give us a regular expression

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]motif = re.compile('[ACGT][ACGT]GATA[AG][ACGT]G')

that can be extracted directly from the iupacdict. Next time, we will check how to create these regex on the fly, from input and the dictionary.