Notes

ORIC (Origin of Replication prokaryotes .. aka Bacteria here.):
==> ORIC is the place where the replication start
==> Its around 500 nucleotides long
==> Oric appears near the DNA-A (a 9 nucleotide long sequence which appears very close to each other)
==> These sequences are highly conserved
==> The initiator protein attaches to the place where DNA-A boxes appears
==> They are unique to each bacteria


BACTERIAL REPLICATION:
==> Its chromosome is circular
==> somewhere the ORIC appears and replication starts
==> Two replication forks are created
==> End of the process is called as Replication Terminus
==> DNA Polymerase does not wait for the entire DNA to unwind the replication process start and the DNA unwinding takes place simultaneously
==> Forward Half strand:
--> DNA polymerase must wait until the replication fork has opened then the DNA Polymerase copies nucleotides as the primers gets attached (OKAZAKI FRAGMENTATION)
--> Replication begins at the ORIC (Multiples ORICs because of OKAZAKI fragmentation)
--> Slow process (fragmentation happens for 2000 nucleotides
==> Reverse Half Strand
--> DNA Polymerase copies nucleotides non stop from 3' to 5' direction (Its the reverse half strand)
--> Replication begins at the ORIC (Only one ORIC present)
==> DNA ligase stitches Okazaki fragments together.
==> Two intact daughter chromosomes are formed
==> Each consist of one parent strand and one newly synthesized daughter strand



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**Computational Approach**
--> Compute how many times each k mer appear in a given DNA string
--> Select the ones with highest frequency.
--> Multiple DNA-A boxes are checked then pattern is matched
--> Once we find the close appearance of the pattern (CLUMP) we can conclude that the origin will happen from that place

function:
Count(Text, Pattern)
return: max(Text, Pattern) %% K-mer with max appearance
--> KMER = substrings of length contained within a biological sequence

// CODE
def count_kmers(read, k):
"""
Parameters
----------
read : string
A single DNA sequence.
k : int
The value of k for which to count kmers.
"""
counts = {}
num_kmers = len(read) - k + 1
for i in range(num_kmers):
kmer = read[i:i+k]
if kmer not in counts:
counts[kmer] = 0
counts[kmer] += 1
return counts

# Single sequence
count_kmers("GATGAT",3)
count_kmers("GATGAT",2)

# Array of sequence
count_kmers(["GATGAT", "GATGAT", "CCGAT"],3)
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