Fabry:Sequence-based analyses/Journal

Fabry Disease » Sequence-based analyses » Journal

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Quidquid latine dictum sit, altum sonatur.

- Whatever is said in Latin sounds profound.

TODO for Julia: Add links to scripts! --Rackersederj 13:27, 12 May 2012 (UTC)

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]

All pictures were autogenerated by the databases and programs. We executed an extra Polyphobius online search for each protein to obtain additional data and plots.

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:

(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]