Fabry:Sequence-based analyses/Journal

Fabry Disease » Sequence-based analyses » Journal

---

Quidquid latine dictum sit, altum sonatur.

- Whatever is said in Latin sounds profound.

Transmembrane helices

First we obtained the fasta sequences with the help of the bash script get_sequences.sh

./get_sequences.sh

With these sequences we carried out a blast search, using Polyphobius' blastget. The output we used for a multiple sequence alignment derived from Kalign and used this MSA as input for PolyPhobius. All this was done with the script call_polyphobius.sh

./call_polyphobius.sh

Most of the pictures were autogenerated by the databases and programs. We executed an extra Polyphobius online search for each protein to obtain additional data and plots.
For plotting the comparison of the length distribution, we used the R script length_distr.R

R CMD BATCH length_distr.R

Signal peptides

Again, we obtained the fasta files for the given proteins and our own desease causing AGAL with a script called get_sequences_sp.sh

./get_sequences_sp.sh

Since by the time we worked on SignalP, the version 4.0 was not working yet, we used the SignalP server, version 4.0.
To gain additional information we performed another Polyphobius prediction with all proteins.

./call_polyphobius_sp.sh

For better demonstration, we depicted Serum Albumin's signal peptide in Pymol using following commands:

orient
hide everything,all
show cartoon, all

color cyan, ss h
color yellow, ss s
color purple, ss "" 

select signPep, resi 1-18
color red, signPep

bg_color gray70
ray 
(see create_pic_pdb.txt)

Besides from that all pictures were obtained from databases and programs.

GO terms

Since all predictions were performed online, no script was used. We used the R Script protfun_category_barplots.R to illustrate the results.

R CMD BATCH protfun_category_barplots.R