PredyFlexy software 1.3.1
1- A first test
"python pred.py -t" allows testing the prediction tool. the sentence "Congratulations FlexyPredy works correctly" show you it works correctly.2- Usage
usage is python "pred.py --help" an example can be easily done with "python pred.py -f DATA/TEST/Prot_0.fasta" [In fact for the output, you must do "python pred.py -f DATA/TEST/Prot_0.fasta --confidence --flex"] the prediction will be find in the subdirectories of TMP[numbers]/PRED-FINAL/predictions.txtidentifiers | >10MHA_0 <---/ [...] <--- first aa are not predicted ---amino acids -- confidence index / / 11 G 47 93 4 3 75 15 1 0.979 0.522 12 L 4 34 79 114 58 13 0 0.130 -0.027 13 R 92 96 95 57 89 15 0 0.209 0.080 14 F 57 96 95 106 55 13 0 -0.183 -0.367 15 I 79 56 58 107 8 15 0 -0.390 -0.415 16 D 57 107 55 43 95 13 0 0.032 -0.131 17 L 11 79 12 64 44 10 0 -0.004 0.025 18 F 42 11 12 110 117 10 0 -0.011 0.195 | | | | | | | \ / / \ \ | / / / \ / number \ \ | / / flexibility flexibility -5 prediced -- index profils prototypes (RMSf and B-factors)Please not an important number of options (some are dedicated to blast, ...):
Usage: pred.py -f the-fasta-file [options]
Options: -h, --help show this help message and exit -f FILENAME, --file=FILENAME obligatory [no default] -o OUTNAME, --output=OUTNAME the name of the files [#NA] -D DIROUTPUT, --DIR=DIROUTPUT the temporary directory [default = /TMP] -c CPU_NUMBERS, --cpu=CPU_NUMBERS number of cpus to be used [default = all] --confidence to compute the confidence index [default=NO] --flex prediction of flexibility [default=NO] -t, --test test [default=NO] [na] --PSIBLASTDIR=PSIBLAST_DIRECTORY directory of psi-blast [default: SOFTS/psiblast] --PSIBLASTdb=PSIBLAST_DB databank of psi-blast (formatted) [SOFTS/db] --PsBround=NB_ROUND psi-blast number of round [default = 4] --PsBeval=E_VALUE psi-blast e-value [default = 0.0001] --PsBval=PSB_VALUE psi-blast value [default = 0.0001] --Makemat=MAKEMAT_DIRECTORY directory of makemat [default: SOFTS/makemat] --GCM=GETMAT_DIRECTORY directory of get_clean_matrix [default: SOFTS/] --SVMclassify=SVMCLASSIFY_DIRECTORY directory of SVM classify [default: SOFTS/] --SVMscale=SVMSCALE_DIRECTORY directory of SVM scale [default: SOFTS/] -q, --quiet say nothing [not default] -v, --verbose verbose [default] -w, --very-verbose terribly verbose [not default] -n, --noban No ban [default: one] --firefox firefox [not default]Default parameters have been optimized and corresponds to the results of the papers [1, 2, 3].
3- It does not work properly
Please check the versions of the different tools- "blastpgp --help" must be blastpgp 2.2.9
blastpgp 2.2.9 arguments: [...]
- be sure to use the swissprot databank of 2009
- go in SOFTS directory to test "./svm_classify", it must be SVM-light V6.01.
> SVM-light V6.01: Support Vector Machine, classification module 01.09.04
- go in SOFTS directory to test "./svm-scale"
usage: ./svm-scale [-l lower] [-u upper] [-y y_lower y_upper] [-s save_filename] [-r restore_filename] filename (default: lower = -1, upper = 1, no y scaling)"
4- I've not the right version of the tool(s).
Please search again on the web. Otherway, copies can be found in the subdirectory subdirectory download/external_src/ where you have download the archives of predyflexy1.1.tar.gz5- get_clean_matrix can be compiled again if needed
cd src/ cc get_clean_matrix.c -o ../SOFTS/get_clean_matrix
6- I've problems with CPUs.
As the prediction is quite long due to the use of 120 SVMs for the prediction of LSPs [1], the number of CPUs used is given as 4.Please change it to you number of avalaible CPUs with the option " -c CPU_NUMBERS, --cpu=CPU_NUMBER"
7- Why my nice results is in a strange directory named TMP18196054366918182720 (or similar name)?
By default a random number is add to TMP.... subdirectory results. You can change it by using the option "D DIROUTPUT, --DIR=DIROUTPUT".8- How to be sure everything is done properly?
An important number of checking is done, you must see (verbose mode ON):Fasta sequence done CPU(s) used: 4 test of softwares done PSI-BLAST done scaling done prediction done confidence index computed flexibility prediction doneand everything must conclude with:
End of loops !!!
9- I see many options for psi-blast. Which ones can I change?
The tools are provided as it. You can do whatever you want. But as said the great contemporary philosopher MC Hammer, U Can't Touch This . SVM parameters have been optimized using specific parameters for BLAST, if you change it, you change the way the prediction will be done. Don't tell us after this .10- I still have questions
Please contact us, see contact page.Some references
- Bornot A., Etchebest C., de Brevern A.G.
A new prediction strategy for long local protein structures using an original description
Proteins (2009) 76(3):570-87.
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Bornot A., Etchebest C., de Brevern A.G.
Predicting Protein Flexibility through the Prediction of Local Structures.
Proteins (2011)79(3):839-52.
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de Brevern A.G.*, Bornot A.*, Craveur P., Etchebest C., Gelly J.-C.
PredyFlexy: Flexibility and Local Structure prediction from sequence
Nucleic Acid Res (2012) 40:W317-22.
*: authors contribute equally.
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Narwani T.J.*.,Etchebest C.*, Craveur P., Leonard S., Rebehmed J., Bornot A., Gelly J.-C., de Brevern A.G.
in silico prediction of protein flexibility with local structure approach
submitted (2016) .
*: authors contribute equally.
Alexandre G. de Brevern
Last Modification : July 2016