ProSAT 1.0

PROtein reSidue Annotation Toolkit

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LICENSE TYPE:
Freely Distributable
USER RATING:
UNRATED
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DEVELOPED BY:
Huzefa Rangwala and George Karypis
HOMEPAGE:
bio.dtc.umn.edu
CATEGORY:
ROOT \ Science and Engineering \ Bioinformatics
1 ProSAT Screenshot:
ProSAT - Usage message
ProSAT is a set of programs that allow building SVM based models for annotating amino acid residues in protein sequences using user supplied features (like PSI-BLAST profiles, or PSIPred profiles). In particular, the toolkit builds features using a window around the residue, and is equipped with a specialized kernel function (normalized second order exponential kernel function nsoe ) along with the standard svm kernel function.

 * ProSAT_Learn is the program to learn "n" one-versus-rest classification models, where n are the possible number of annotations. It can also learn a support vector regression model to predict a floating point value.

 * ProSAT_Predict is the program to predict the annotation for each residue from the built models, and output a L x n dimension profile, outputting the score from each of the n one-versus-rest SVM models for each amino acid residue and L is the length of the protein sequence. In case of a regression model, n =1

 * ProSAT_Eval is the program to evaluate the various parameters like kernel, window lengths, and regularization parameters. ProSAT_Eval automatically performs cross validation and reports the standard classification and regression performance. Please use the perl script cv_script.pl to automatically perform model selection and training the best classification or regression model for the problem.

Last updated on October 14th, 2010

#SVM models #amino acid residues #protein sequence #SVM #models #builder #amino

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