HOW TO USE:

To use this code, you must have the following requirements: Python 3+ HMMER 2.3.2

Download the code. In the same folder that contains "main", have a folder with the following names: analysis chromosomes hmmer output

Databases:

There should be a folder named databases present. Unzip the folder. Next, download variant_summary.txt from clinvar: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/. Drag it into the folder and unzip it.

HMMER:

There should be a folder named HMMER present. Unzip the folder.

Analysis:

This folder is used to compare the predicted change in DNA-binding specificity. To do this, visit zf.princeton.edu and click "Predict PWS". Type in the ZF protein sequence and click send. Click on the appropiate ZF domain and change the prediction model to be Polynomnial SVM. Click submit and download the PWM. Save the file in the following format:

GeneName_DomainNumber_o.txt - for an original gene. GeneName_DomainNumber_m.txt - for a mutated gene.

The files are already included in the folder; just unzip the folder.

Chromosomes: This folder is used to store the chromosomes. Chromsomes can be downloaded from: ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/

Finally, run project.py as a script to get the main output files. There are other functions in the file that can do a variety of things. Feel free to explore. If you have any questions, please email me at as2779[at]cornell.edu.