Difference between revisions of "Fabry:Homology based structure predictions/Journal"
From Bioinformatikpedia
Rackersederj (talk | contribs) m |
Rackersederj (talk | contribs) (→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. |
||
| + | 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 [https://www.dropbox.com/s/8vu2mnnl733f3zh/make_dataset_hhpred.pl.txt make_dataset_hhpred.pl] [https://www.dropbox.com/s/4ue1umheukk7j1a/hhpred.out.txt hhpred.out] 0.0000000000000001 |
||
| + | This resulted in the HHpred datasets mentioned in [[Fabry:Homology_based_structure_predictions#Dataset_preparation | Dataset preparation]] Table 1 |
||
| + | perl [https://www.dropbox.com/s/vul8gare1lgwgk5/make_dataset_coma.pl.txt make_dataset_coma.pl] [https://www.dropbox.com/s/ycfy8ke6xt3ofrp/coma.out.txt coma.out] 0.002 |
||
| + | This resulted in the Coma datasets mentioned in [[Fabry:Homology_based_structure_predictions#Dataset_preparation | Dataset preparation]] Table 2 |
||
== Calculation of models == |
== Calculation of models == |
||
Revision as of 23:55, 22 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. 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
perl make_dataset_coma.pl coma.out 0.002
This resulted in the Coma datasets mentioned in Dataset preparation Table 2
