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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 PDB protein databank at NTHU
BLAST against Motif/Domain database at NTHU
Search your protein or DNA sequence against Motif/Domain database.
BLAST against customized database (the databases built by yourself)
[NHRI, Sinica]
   

Downloadable Analysis Tools

   
Software for two-channel cell-based RNAi data [NHRI]
A software platform for GEnome-scale Metabolic model Simulation, Reconstruction and Visualization, GEMSiRV
A software for contig Integrator for Sequence Assembly [NHRI]

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

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

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

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

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

   

Sequence Analysis

Analysis Tools for Influzena Virus Surveillance [NHRI]
For influenza urveillance, both antigenic and genetic analyses of influenza isolates are routinely carried out to monitor changes in surface antigens, and ATIVS consist of analyzing both serology data and HA1 sequence data of influenza A/H3N2 viruses.
Manual
Prediction of protein subcellular localization [NCTU]
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 [NCTU]  
Web-based Multiple Sequence Alignment [NTHU]
ClustalW is a widely used multiple sequence alignment computer program. This is a customized ClustalW tool supported by NTHU bioinformatics center.
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 [Sinica, NHRI]
ENACE System is an identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.
A Web interface for visualizing ESTs [Sinica, NHRI]
A Web interface for visualizing mouse, rat, cattle, pig, and chicken conserved ESTs in human genes and human alternatively spliced variants.
Web-based gene prediction service [NTHU]
A web interface gene prediction program for prokaryotic genome sequence
Manual
Predict phosphorylation sites within given protein sequences [NCTU]
KinasePhos is to computationally predict phosphorylation sites within given protein sequences. It has higher accuracy and provides not only the location of the phosphorylation sites, but also the corresponding catalytic protein kinases.
Manual
Multiple Sequence Alignment with Constraints [NCTU]
MuSiC is a web server to perform the constrained alignment of a set of sequences, such that the user-specified residues/nucleotides are aligned with each other.
Manual
Primer Design Assistant [NHRI]
Primer Design Assistant (PDA) is a web interface primer design service combined with thermodynamic theory to evaluate the fitness of primers.
Manual
An Alternative Splicing Database based on Protein, mRNA, and EST Sequences [NCTU]
ProSplicer, is a putative alternative splicing database which stores alternative splicing information. These information are produced from variant proteins and expression patterns of a gene. Protein sequences, messenger RNA and expressed sequence tags (ESTs) provide valuable information about splice variants of genes.
Manual
A Comparative Method for Identification of Gene Structures and Alternatively Spliced Variants [Sinica, NHRI]  
A Regulatory RNA Motifs and Elements Finder [NCTU]
RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence.
Manual
An information repository for mRNA alternative splicing in human genome [NCTU]
SpliceInfo is a database which provides a means of investigating alternative splicing and can be used for identifying alternative splicing - related motifs, such as the exonic splicing enhancer (ESE), the exonic splicing silencer (ESS) and other intronic splicing motifs.
Manual
Identify conserved sequence elements associated to mRNA splicing [NCTU]
Unique Probe Selector [Sinica, NHRI]
The UPS evaluates probe-to-target hybridization under a user-defined condition in silico to ensure high-performance hybridization and minimizes the possibility of non-specific reactions.
Manual

Comparative Genomics

Web tool for Mammalian Phenotype Enrichment Analysis [NHRI]
Phenotype for enrichment analysis for gene sets abtained from mammalian -omics studies.
Manual
Drosophila phenotype enrichment analysis for insect functional genomics Manual
     

Phylogenetic Analysis

Phylogenetic reconstruction by Automatic Likelihood Model selector [Sinica, NHRI]
PALM is aiming at providing biologists for automatically computing, comparing and selecting the best model among various DNA (JC69, K80, F81, HKY, TrN, GTR) and Protein (JTT, MtREV, MtMam, MtArt, Dayhoff, WAG, RtREV, CpREV, Blosum62, VT, HIVb, HIVw) models of molecular biological evolution that best fits the given biological sequences.
Manual
Phylogenetic Web Repeater [NHRI]
PhylOgenetic WEb Repeater (POWER), a web-based service, is designed to perform phylogenetic analysis of proteins and DNA sequences.
Manual
     

Structural Analysis ( Structural Biology tools/database )

Protein Structure Prediction Server [NCTU]
(PS)2 is an automated homology modeling server. The method uses an effective consensus strategy by combining PSI-BLAST, IMPALA, and T-Coffee in both template selection and target-template alignment.
Manual
Protein structure search [NCTU]
3D-BLAST is a very fast and accurate method for discovering the homologous proteins and evolutionary classifications of a newly determined protein structure.
Manual
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 [NCTU]
GEMDOCK is a program for computing a ligand comformation and orientation relative to the active site of target protein.
Manual
Integrated Service of Structure Similarity Search Aided by Ramachandran Sequential Transformation [NTHU]
In this service, we implement two protein structural similarity search methods, SARST and CPSARST, and allows the user to input many structures at once. Its MPI system will do the similarity searches and structural alignments in a batch mode to rapidly retrieve structural homologs of the query proteins.
Structure Alignment by Ramachandran Search Tool [NTHU]
SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools.
 
Sequence Derived Structure Entropy [NCTU]  
Structural Entropy Query [NCTU]
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 [NTHU] Manual
   

Miscellaneous Tools

A Java plugin for Cytoscape [Sinica, NHRI] Manual
European Molecular Biology Open Software Suite [NHRI]  
EMBOSS Graphical User Interface: EMBOSS explorer at NHRI
Java user interface of EMBOSS at NHRI Manual FAQ Application
Wisconsin Sequence Analysis Package [NHRI] Manual FAQ Application
Hub OBjects Analyser, a web-based service designed to explore the essential nodes in a network [Sinica, NHRI] Manual
KEGG Pathway Search Tool [NTHU]
KPST is a lite search engine for KEGG pathway database. Users can do the search by specifying organism or metabolic pathway; besides, a key word search from organism is also available.
Manual
Reniforced Merging Algorithms [NTHU] Manual
Web-based GCG [NHRI] Manual FAQ
   

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