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8 Homology & Similarity

8 Sequence Analysis

ATIVS		Analysis Tools for Influzena Virus Surveillance [NHRI] For influenza surveillance, 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.
CELLO		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.
Chameleon Sequence Finder		Retrive a small peptide fragment sequence from a collection of PDB sequences [NCTU]
ClustalW		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.
CNVVdb		A database of copy number variations across vertebrate genomes. [Sinica, NHRI] CNVVdb is a web interface for identification of potential inter-species CNV information by finding duplicated regions within a genome (paralogues) and between different genomes (orthologues)
ENACE System		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.
ESTviewer		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.
GenePredict		Web-based gene prediction service [NTHU] A web interface gene prediction program for prokaryotic genome sequence
KinasePhos		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.
MuSiC		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.
PDA		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.
ProSplicer		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.
PSEP System		A Comparative Method for Identification of Gene Structures and Alternatively Spliced Variants [Sinica, NHRI]
RegRNA		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.
RNAMST		An efficient and flexible search tool for RNA structural homologs [NCTU] RNAMST is an efficient and flexible RNA Motif Search Tool for RNA structural homologs. RNAMST web server accepts four different kinds of input formats to facilitate user to describe a RNA structure easily.
SpliceInfo		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.
SpliceMotif		Identify conserved sequence elements associated to mRNA splicing [NCTU]
UPS		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.

8 Phylogenetic Analysis

Palm		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.
POWER		Phylogenetic Web Repeater [NHRI] PhylOgenetic WEb Repeater (POWER), a web-based service, is designed to perform phylogenetic analysis of proteins and DNA sequences.

8 Structural Analysis ( Structural Biology tools/database )

(PS)2		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.
3D-BLAST		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.
CPSARST		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
GEMDOCK		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.
iSARST		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.
SARST		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.
SDSE		Sequence Derived Structure Entropy [NCTU]
StEQ		Structural Entropy Query [NCTU] StEQ is a tool to retrive a small peptide fragment sequence from a collection of PDB sequences.
Tm Predictor		Melting Temperature Prediction : Predict thermal stability of proteins [NTHU]

8 Miscellaneous Tools

Cyto-Hubba		A Java plugin for Cytoscape [Sinica, NHRI]
EMBOSS		European Molecular Biology Open Software Suite [NHRI]
EMBOSS GUI		EMBOSS Graphical User Interface: EMBOSS explorer at NHRI
JEMBOSS		Java user interface of EMBOSS at NHRI
GCG		Wisconsin Sequence Analysis Package [NHRI]
Hubba-Hubba		Hub OBjects Analyser, a web-based service designed to explore the essential nodes in a network [Sinica, NHRI]
KPST		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.
RMA		Reniforced Merging Algorithms [NTHU]
SeqWeb		Web-based GCG [NHRI]

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