This exercise serves as an introduction sequence analysis with regular expressions.
Regular expressions are a mini programming language specific for patterns in sequences, not just biological.
They have been added to most programming languages, like Python, R, C and Perl.
We can use regular expressions to find open reading frames.
Construct a regular expression for finding a start codon and a stop codon separated by a the fewest triplets (groups )
Test you regex with this AAAATGCCCTAAGGGA sequence on regex101.com
X56730.1
The SNF1 kinase regulate proteins by phosphorylation. The gene ACC1/YNR016C encodes the ACC1p acetyl-CoA carboxylase in S. cerevisiae. This is an important step if fatty acid synthesis and the ACC1p is deactivated by phosphorylation. The SNF1 kinase recognizes a a pecific pattern (motif) in the protein sequence and phosphorylates a specific serine amino acid.
” target motif, … is a hydrophobic residue (M, L, F, I or V) for P-5 and P + 4, and basic residues (R, K or H) for P-3 or P-4
The P- or P+ indicate positions relative to the Serine.
-----S----
5432101234
Construct the regular expression to look for this motif.
How many SNF1 motifs can you find in the ACC1 protein sequence and where are they located?