TDP43-analysis

Source code for:

----- Vertebrate TDP43 sequence analysis -----

1.) Compiling NTD, RRM and CTD databases from a collection of vertebrate TDP43 homologs (Step 1)
Input: Vertebrate TDP43.fasta
Analysis: Step1.nb
Output: NTDs.fasta, RRMs.fasta, CTDs.fasta

2.) Isoform filter to ensure single sequence per filter (Step 2)
Input: NTDs.fasta, RRMs.fasta, CTDs.fasta
Analysis: Step2.nb
Output: Unique species NTDs.fasta, Unique species RRMs.fasta, Unique species CTDs.fasta

3.) Analyzing the databases (Step 3)
Input: Unique species NTDs.fasta, Unique species RRMs.fasta, Unique species CTDs.fasta
Analysis: Step3.nb

4.) Subdividing the CTD database into IDR and CR databases (Step 4)
Input: Unique species CTDs.fasta
Analysis: Step4.nb
Output: IDR1 Domains.fasta, IDR2 Domains.fasta, Conserved Regions.fasta

5.) Analyzing the IDR and CR databases (Step 5)
Input: IDR1 Domains.fasta, IDR2 Domains.fasta, Conserved Regions.fasta
Analysis: Step5.nb

6.) Spacing of hydrophobic residues (Step 6)
Input: IDR1 Domains.fasta, IDR2 Domains.fasta
Analysis: Step5.nb

7.) Sliding window analysis of CTD sequences (Step 7)
Input: Unique species CTDs.fasta
Analysis: Step7.nb

8.) Residual analysis (Step 8)
Input: IDR1 domains.fasta, IDR2 domains.fasta
Analysis: Step8.nb


----- TDP43 splicing reporter analysis -----

Input: fcs files
Analysis: CSA_Gating.nb, CSA_Plotting


----- TDP43 RRM-GFP droplet formation analysis -----

Input: image files
Analysis: DropletAnalysis.nb