MirAlign

An online tool to identify homologous miRNA genes. This tool can search for new miRNA candidates by requiring structural similarity and sequence conservations between new candidates and experimentally identified miRNAs.

MethCGI

MethCGI is a tool to predict the methylation status of CpG islands in the human brain, developed on the data from human brain DNA using support vector machine (SVM).

SubMito

SubMito is the first computational system for predicting protein submitochondria locations from its primary sequence. SubMito is designed and implemented with Java. This site is a web-like front end for SubMito system.

Triplet-SVM

This program is developed for predicting a query sequence with hairpin structure as a real miRNA precursor or not. The triplet-SVM classifier analyzes the triplet elements of the query and predicts it using a SVM classifier. The SVM classifier is previously trained based on the triplet element features of a set of real miRNA precursors and a set of pseudo-miRNA hairpins.

PCS

A stand-alone pakage to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3'-UTRs.

CURE

In angiosperm mitochondria, the genetic information which was encoded in the mitochondrial DNA sequence can be modified at RNA level. Several cytidines of the transcripts can be converted to uridines by a deaminasing process. This type of C-to-U RNA editing has very high site slectivity. The mechanism for selecting the editing site is still unknown. CURE (Cytidine-to-Uridine Recognizing Editor) is a computational tool which predicts C-to-U RNA editing sites using evolutionary information.

PhoScan

Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach.

OSCAR

OSCAR (One-class SVM for Cis-elements Accurate Recognition) is a program that can be used to identify binding sites of known transcription factors on promoter regions. The algorithm is based on one-class support vector machine (One-class SVM). OSCAR uses the sequential compositoin of known binding sites, and further incorporates the locational preferences of binding events.

TAGS

TAGS is a tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations