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
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Source code for sequence analysis of vertebrate TDP43 homologs
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