contra.stanford.edu
CONTRA: CONditional TRAining for Biological Sequence AnalysisA collection of biosequence analysis programs based on CRFs.
http://contra.stanford.edu/
A collection of biosequence analysis programs based on CRFs.
http://contra.stanford.edu/
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CONTRA: CONditional TRAining for Biological Sequence Analysis | contra.stanford.edu Reviews
https://contra.stanford.edu
A collection of biosequence analysis programs based on CRFs.
contra.stanford.edu
CONTRAfold: CONditional TRAining for RNA Secondary Structure Prediction
http://contra.stanford.edu/contrafold
CONTRAST: CONditionally TRAined Search for Transcripts
http://contra.stanford.edu/contrast
CONTRAST predicts protein-coding genes from a multiple genomic alignment using a combination of discriminative machine learning techniques. A two-stage approach is used, in which output from local classifiers is combined with a global model of gene structure. CONTRAST is trained using a novel procedure designed to maximize expected coding region boundary detection accuracy.
CONTRAlign: CONditional TRAining for Protein Sequence Alignment
http://contra.stanford.edu/contralign
CONTRAlign is an extensible and fully automatic parameter learning framework for protein pairwise sequence alignment based on pair conditional random fields. The CONTRAlign framework enables the development of feature-rich alignment models which generalize well to previously unseen sequences and avoid overfitting by controlling model complexity through regularization.
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Software | The Hudson Valley RNA Club
http://www.hudsonvalleyrnaclub.org/software
The Hudson Valley RNA Club. Software for analyzing the hypothetical secondary structure of a family of homologous RNA, predicting if there is a shared secondary structure, and predicting the folded stems in it. The input is a set of single-stranded RNA sequences that need not to be aligned. A thermodynamic model with energy minimization combined with locally conserved primary structure and sequence covariations is used. CONTRA (CONditional TRAining for biosequence analysis) is a software project that app...
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CONTRA: CONditional TRAining for Biological Sequence Analysis
The CONTRA (CONditional TRAining for Biosequence Analysis) Project is a collection of programs which apply discriminatively-trained probabilistic models (specifically conditional random fields and their variants) to a diverse array of sequence labeling problems in bioinformatics. Currently, the CONTRA family includes:. A protein sequence aligner. An RNA secondary structure folder. A multiple sequence de novo gene predictor.
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