Difference between revisions of "Fabry:Homology based structure predictions/Journal"
From Bioinformatikpedia
Rackersederj (talk | contribs) m (→Dataset preparation) |
Rackersederj (talk | contribs) m (→Dataset preparation) |
||
| Line 3: | Line 3: | ||
== Dataset preparation == |
== Dataset preparation == |
||
| − | The homology search was performed online and resulted in the two output files [https://www.dropbox.com/s/4ue1umheukk7j1a/hhpred.out.txt hhpred.out] and [https://www.dropbox.com/s/ycfy8ke6xt3ofrp/coma.out.txt coma.out] for the structure search with [http://toolkit.tuebingen.mpg.de/hhpred HHpred] and [http://bioinformatics.ibt.lt:8085/coma/ COMA], respectively. |
+ | The homology search was performed online and resulted in the two output files [https://www.dropbox.com/s/4ue1umheukk7j1a/hhpred.out.txt hhpred.out] and [https://www.dropbox.com/s/ycfy8ke6xt3ofrp/coma.out.txt coma.out] for the structure search with [http://toolkit.tuebingen.mpg.de/hhpred HHpred] and [http://bioinformatics.ibt.lt:8085/coma/ COMA], respectively. In both cases, we used the default values, thresholds and databases.<br> |
From these two files we tried in each case to create three distinct datasets with the demanded sequence identity to the target protein with the following calls and scripts. |
From these two files we tried in each case to create three distinct datasets with the demanded sequence identity to the target protein with the following calls and scripts. |
||
Revision as of 01:01, 23 May 2012
Fabry Disease » Homology based structure predictions » Journal
Contents
Dataset preparation
The homology search was performed online and resulted in the two output files hhpred.out and coma.out for the structure search with HHpred and COMA, respectively. In both cases, we used the default values, thresholds and databases.
From these two files we tried in each case to create three distinct datasets with the demanded sequence identity to the target protein with the following calls and scripts.
perl make_dataset_hhpred.pl hhpred.out 0.0000000000000001
This resulted in the HHpred datasets mentioned in Dataset preparation Table 1 and the corresponding pdb structure files.
perl make_dataset_coma.pl coma.out 0.002
This resulted in the Coma datasets mentioned in Dataset preparation Table 2 and the corresponding pdb structure files.
