oriC

Predicting oriC in plasmids and chromosomes.

See ../oriC/APInotes for usage directions

Fetching Sequences

• See oriC/fetch_genome.py for fetching entire genomic sequence of
  an organism

• See oriC/fetch_oric.py for fetching only oric sequence of an organism

In either case the sequence data is stored in data/ directory.

The OriC Computational Problem

INPUT : A DNA string (genome)
OUTPUT: Location of oriC in it

Why is it important to know oriC ?

• To understand cell replication.
• To create biomedical therapies like viral vectors
• ...

Bacterial Genome

Model organism Vibrio cholerae with known oriC sequence.

How does replication initiate?
Initiation of replication begins with DnaA, a protein that binds to
a short segemento of the oriC known as the Dna Box

The DnaA Box tells the DnaA to essentially bind there.

The key question then is to ask:

How to find this DnaA Box without knowing what it looks like?

LINK TO NCBI FTP SERVER

https://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/

References

• Bioinformatics Algorithms Vol 1 (Book)
• Ori-Finder
• Cumulative-Skew
• UNC-BioAlgorithms