PSI Genomic Resources

 

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Tools

Machine Learning
Affinity Propagation  
Affinity propagation is an algorithm that identifies exemplars among data points and forms clusters of data points around these exemplars. It operates by simultaneously considering all data point as potential exemplars and exchanging messages between data points until a good set of exemplars and clusters emerges (See BJ Frey and D Dueck, Science 315, Feb 16, 2007). Click here for more information.
 
Sequence Analysis
GenASAP   protected resources, login required
GenASAP is a generative model for finding alternative splicing isoforms.
SeedSearcher   protected resources, login required
SeedSearcher is a simple hyper-geometric approach for discovering putative transcription factor binding sites. It provides an economic yet effective method for finding statistical significance in given sequence data.
SeedAnalysis   protected resources, login required
SeedAnalysis is a set of scripts for post-processing the results of SeedSearcher. It generates images, graphs, HTML pages and other format data files.
LearnPSSM   protected resources, login required
LearnPSSM is a program for discriminative learning of position specific scoring matrix (PSSM) motifs in a probabilistic framework. It gets as input a set of sequences and matching prior beliefs (weights between 0 and 1) for each sequence being regulated/containing an unknown cis element(s). The motif learning is initiated from a single or multiple PSSM motifs. These initial motifs can be either specified directly by the user or extracted from a preliminary SeedSearcher run on the data set.
 
Miscellaneous
Repository   protected resources, login required
This is an internal data repository for important data backup. It provides a convenient web interface to configure data types and data properties; to upload, search, browse and download data items. It also allows you to keep versions.