notes

Paper1
1. No-strand-bias conditions
2. Q - what is equilibrium point?
Paper2
1. Sources of strand compositional asymmetry?
2. Why not A-T skew?
3. What is template and coding strand?
4. 
Paper3 - Cumulative skew
1. Trade-off- large vs small window size
2. Note that SOME OF THE LOCAL POLARITY SWITCHES ARE IMPORTANT
3. Do a CUMULATIVE skew - sum/INTEGRATE over the windows from start to current
4. Max value at terminus, min at ori

We are concerned with finding the origin of replication

Auto-correlation, cumulative skew OR iCorr.


Cumulative skew revisited
1. Genome rearrangements?
2. The skew, calculated as (G–C)/(G+C) for a window sliding along the sequence, was shown to switch polarity in the vicinity of the terminus (ter) and origin (ori) of replication,
3. Such plots may not always be very illustrative due to visible fluctuations for a small window size, while larger windows may hide precise coordinates of polarity switches
4. Use CUMULATIVE over several windows
5.  distances between global extremities are very close to 50% of the respective genome lengths and the minimum is always located at the origin
6. Genome rearragements
7. Different replication mechanism leads to parabolic curve
8. Little is known about archaea