Difference between revisions of "Fabry:Sequence-based analyses/Journal"
Rackersederj (talk | contribs) (→GO terms) |
Staniewski (talk | contribs) (Add links to scripts) |
||
| Line 7: | Line 7: | ||
::- Whatever is said in Latin sounds profound. |
::- Whatever is said in Latin sounds profound. |
||
| − | TODO for Julia: Add links to scripts! --[[User:Rackersederj|Rackersederj]] 13:27, 12 May 2012 (UTC) |
||
== Secondary structure == |
== Secondary structure == |
||
| Line 14: | Line 13: | ||
== Transmembrane helices == |
== Transmembrane helices == |
||
| − | First we obtained the fasta sequences with the help of the bash script [ get_sequences.sh] |
+ | First we obtained the fasta sequences with the help of the bash script [https://dl.dropbox.com/u/13796643/fabry/seq_analysis_scripts/get_sequences.sh.html get_sequences.sh] |
| + | ./<span class="plainlinks">[https://dl.dropbox.com/u/13796643/fabry/seq_analysis_scripts/get_sequences.sh.html get_sequences.sh]</span> |
||
| − | ./[ 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] |
+ | 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 [https://dl.dropbox.com/u/13796643/fabry/seq_analysis_scripts/call_polyphobius.sh.html call_polyphobius.sh] |
| + | ./<span class="plainlinks">[https://dl.dropbox.com/u/13796643/fabry/seq_analysis_scripts/call_polyphobius.sh.html call_polyphobius.sh]</span> |
||
| − | ./[ 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. |
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 == |
== 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] |
+ | Again, we obtained the fasta files for the given proteins and our own desease causing AGAL with a script called [https://dl.dropbox.com/u/13796643/fabry/seq_analysis_scripts/get_sequences_sp.sh.html get_sequences_sp.sh] |
| + | ./<span class="plainlinks">[https://dl.dropbox.com/u/13796643/fabry/seq_analysis_scripts/get_sequences_sp.sh.html get_sequences_sp.sh]</span> |
||
| − | ./[ get_sequences_sp.sh] |
||
Since by the time we worked on SignalP, the version 4.0 was not working yet, we used the [http://www.cbs.dtu.dk/services/SignalP/ SignalP] server, version 4.0. <br> |
Since by the time we worked on SignalP, the version 4.0 was not working yet, we used the [http://www.cbs.dtu.dk/services/SignalP/ SignalP] server, version 4.0. <br> |
||
To gain additional information we performed another Polyphobius prediction with all proteins. |
To gain additional information we performed another Polyphobius prediction with all proteins. |
||
| + | ./<span class="plainlinks">[https://dl.dropbox.com/u/13796643/fabry/seq_analysis_scripts/call_polyphobius_sp.sh.html call_polyphobius_sp.sh]</span> |
||
| − | ./[ call_polyphobius_sp.sh] |
||
For better demonstration, we depicted Serum Albumin's signal peptide in Pymol using following commands: |
For better demonstration, we depicted Serum Albumin's signal peptide in Pymol using following commands: |
||
(see create_pic_pdb.txt) |
(see create_pic_pdb.txt) |
||
| Line 34: | Line 33: | ||
== GO terms == |
== GO terms == |
||
Since all predictions were performed online, no script was used. |
Since all predictions were performed online, no script was used. |
||
| − | We used the R Script [ protfun_category_barplots.R] to illustrate the results. |
+ | We used the R Script [https://dl.dropbox.com/u/13796643/fabry/seq_analysis_scripts/protfun_category_barplots.R.html protfun_category_barplots.R] to illustrate the results. |
| − | R CMD BATCH [ protfun_category_barplots.R] |
+ | R CMD BATCH <span class="plainlinks">[https://dl.dropbox.com/u/13796643/fabry/seq_analysis_scripts/protfun_category_barplots.R.html protfun_category_barplots.R]</span> |
Revision as of 21:27, 12 May 2012
Fabry Disease » Sequence-based analyses » Journal
Quidquid latine dictum sit, altum sonatur.
- - Whatever is said in Latin sounds profound.
Secondary structure
Disorder
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
