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Cancer Risk Prediction Tool

Risk prediction models for lung cancer. Taiwan Never-smoking females Lung cancer risk calculator. [NHRI]
   

Downloadable Analysis Tools

 

A fast and accurate RNA-seq mapper with a divide and conquer strategy

A software platform for GEnome-scale Metabolic model Simulation, Reconstruction and Visualization

Modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem

An ultra-fast sequence alignment algorithm for intra-species genome comparison

A high quality biomedical annotation corpus for the development of natural language processing technique

An automated analysis tool for label-free quantitative proteomics [IASL]

Generic Evolutionary Method for molecular DOCKing

Integrated Service of Structure Similarity Search Aided by Ramachandran Sequential Transformation

A divide-and-conquer algorithm for NGS read mapping with high error tolerance

Prediction tool of kinase-specific phosphorylation sites

An automated tool for glycopeptide identification and glycan composition determination [IASL]

An efficient and versatile approach for short-read mapping and variant identification using high-throughput sequenced data.

An automated quantitation tool, which utilizes XICs acquired from isotope labeling techniques for quantitation analysis [IASL]

MetastasisWay attempts to construct metastatic pathways by integrating the extensive information within the large collection of research papers. [IASL]

An automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling method [IASL]

An automatic neuronal morphology quantification method.

The Plant Promoter Analysis Navigator is a practical resource for detecting transcription factor binding sites (TFBSs) based on TFBS position weight matrices (PWMs) collected from public resources and experimental ChIP-seq datasets. PlantPAN also provides the TF information and their corresponding TFBSs, deposition of histone marks, CpG islands, and tandem repeats on plant promoter sequences.

Software for two-channel cell-based RNAi data

A highly accurate Metagenomic strain-level profiling tool

A transformer-based prediction tool for AMPs with different functional activities

   

Functional Genomics

Prediction tool of antiviral peptides
Web tool for identifying multi-drug resistance of Staphylococcus aureus based on MALTI-TOF MS spectra
Model organism Phenotype Enrichment Analysis of eukaryotic gene sets Manual
     

Homology & Similarity

BLAST Search at NCKU
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. This is a customized BLAST tool supported by NCKU bioinformatics center.
BLAST against customized database
BLAST against PDB protein databank at NTHU
BLAST against Motif/Domain database at NTHU
   

Miscellaneous Tools

Identify Anti-Cancer Peptides in AI
Identify Anti-Viral Peptides in AI
A web tool for visual summary of mutations in cancer cohorts
A Java plugin for Cytoscape Manual
A galaxy docker for estimation of Expression profiling based on Genome reference in RNA-seq.
Electronic Laboratory Notebook
European Molecular Biology Open Software Suite  
Hub OBjects Analyser Manual
KEGG Pathway Search Tool Manual
A webserver for draft Metabolic network reconstruction for Bacteria.
Reniforced Merging Algorithms Manual
Assembly of protein complexes by integrating graph clustering methods
Smart Genotyping on Upper Respiratory Pathogens in AI
   

Phylogenetic Analysis

Phylogenetic reconstruction by Automatic Likelihood Model selector
Phylogenetic Web Repeater [NHRI]
PhylOgenetic WEb Repeater (POWER), a web-based service, is designed to perform phylogenetic analysis of proteins and DNA sequences.
Manual

Sequence Analysis

 
An Antimicrobial Peptide Predictor in Deep Learning.
Prediction of protein subcellular localization [NYCU]
CELLO is a simple, straightforward implementation of a single module (SVM) based on multiple n-peptide composition to predict subcellular localization.
 
Retrive a small peptide fragment sequence from a collection of PDB sequences [NYCU]  
Contig Integrator for Sequence Assembly of Bacterial Genomes
Web-based Multiple Sequence Alignment Manual
Deep-sequencing small RNA analysis pipeline [NTHU, CGU]
DSAP is a web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA. The functions of DSAP suite include adaptor removal, clustering of tags, classification of non-coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase databases respectively.
Manual
Identification and evolutionary analysis of novel exons and alternative splicing events
A Web interface for visualizing ESTs
FamPipe is a comprehensive analysis pipeline for family data. Monitoring the antigenic evolution of human influenza A viruses to understand how and when viruses escape from existing immunity [NHRI]
Monitoring of human influenza variants
Web-based gene prediction service Manual
Identification of cytotoxic T lymphocyte epitopes for swine viruses
IGOF implements three powerful gene-based gene-gene interaction tests for common, low-frequency, and common with low-frequency variant pairs in case-control studies using next-generation sequencing data. [NHRI]
Web-based Multiple Sequence Alignment Manual
Using Deconvolution Approach to Reveal the Immuno-Microenvironment of Complex Tissues and Tumors from the Transcriptomics
Primer Design Assistant Manual
An Alternative Splicing Database based on Protein, mRNA, and EST Sequences Manual
A Comparative Method for Identification of Gene Structures and Alternatively Spliced Variants  
A Regulatory RNA Motifs and Elements Finder [NYCU]
RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence.
Manual
A sequence-based algorithm for searching circularly permuted proteins
An information repository for mRNA alternative splicing in human genome [NYCU] Manual
Identify conserved sequence elements associated to mRNA splicing [NYCU]
Unique Probe Selector Manual

Structural Analysis ( Structural Biology tools/database )

Protein Structure Prediction Server Manual
Protein structure search Manual
Circularly-permuted protein structure Predictor
Web server for predicting viable circular permutations in proteins
Circular Permutation Search Aided by Ramachandran Sequential Transformation [NTHU]
CPSARST is an efficient circular permutation search tool applied to the detection of novel protein structural relationships
Generic Evolutionary Method for molecular DOCKing [NYCU]
GEMDOCK is a program for computing a ligand comformation and orientation relative to the active site of target protein.
Manual
Structure Alignment by Ramachandran Search Tool  
Sequence Derived Structure Entropy [NYCU]  
Structural Entropy Query [NYCU]
StEQ is a tool to retrive a small peptide fragment sequence from a collection of PDB sequences.
Manual
Melting Temperature Prediction : Predict thermal stability of proteins Manual
   

Topology Prediction

The protein KNOT web server
   

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