WEN CHEN HW3

 I stopped after finished the INI2 problem, obviously I am stuck in the problem INI3.

And the code can be found in my github: https://github.com/wcchen9447/PLS-599/blob/master/Rosalind-Variables%20and%20Some%20Arithmetic.txt

 Project:

Aim: to explore the influence of DCL proteins in loading of pol IV dependent siRNAs  to AGO4.

Problem to solve: what do the profiles of pol IV dependent siRNAs bound to AGO4 look like in DCL mutants?

Outline of the project:

1, download the published deep sequencing data of siRNAs either bound to AGO4 in WT col-0, or in different DCL mutants in Arabidopsis;

2, get the siRNA that might load to AGO4 in dcl3 mutant by comparison between different siRNA profiles from different background, using python script and hpc;

3, characterize the siRNAs  that might load to AGO4 in dcl3 mutant by mapping to the col-0 genome sequence and grouping based on their length and origin in genome.

CONCEPT MAP: