Sequence and Signal Analysis


  • BEACON - automated tool for Bacterial gEnome Annotation ComparisON

  • CMsearch - CMsearch is a protein homology detection method that simultaneously explore protein sequence space and protein structure space by cross-modal learning.

  • Dragon Desert Masker (DDM) -  Transcription Initiation Desert Identification

  • Dragon Motif Finder V7 (DMF) - This is a simple ab-initio motif finding tool that allows the processing of relatively large sequence sets in a relatively short amount of time on the web. 

  • Dragon PolyA Spotter (DPS) - This is a predictor of poly(A) motifs within human genomic DNA sequences.

  • Dragon PPRE Spotter - This predicts the DNA binding sites of peroxisome proliferatior-activated receptors (PPARs) with extremely high accuracy that is at least order of magnitude better than the next best system for the same purpose.

  • Dragon Translation initiation site Spotter (DTS) - This application predicts Translation Initiation Sites (TISs) in Arabidopsis genomic sequences provided in fasta format.

  • Histone Modification in Cancer (HMCan) - This  is a set of methods to analayze ChIP-seq data obtained from cancer samples.

  • Hot Spot Prediction - Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences

  • LigandRFs: predict protein-ligand binding sites - This is a random forest-based approach to predict protein-ligand binding sites.

  • Memory-efficient genome assemblers on stand-alone and cloud infrastructures (MEGA) - 

  • miRNAVISA - Explores miRNA families for hypotheses generation

  • Omni-PolyA - A method for accurate recognition of poly(A) signals in human genomic DNA.

  • PhenomeNET Variant Predictor - A phenotype-based tool to annotate and prioritize disease variants in WES and WGS data

  • Predict poly(A) motifs in human DNA sequence - The program is able to predict the 12 main variants of human poly(A) motifs, i.e., AATAAA, ATTAAA, AAAAAG, AAGAAA, TATAAA, AATACA, AGTAAA, ACTAAA, GATAAA, CATAAA, AATATA, and AATAGA.

  • Predict protein-DNA binding affinity - Our method trains a two-round support vector regression model for predicting protein-DNA binding affinity.

  • PROSTA-inter - This is a sequence-order independent alignment tool that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures (protein-protein, protein-DNA, and/or protein-RNA).

  • Readscan - This is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. 

  • TELS - Transcribed Enhancer Landscape Search