Online Tools and Servers

Userful Online Bioinformatics Tools

Sequence Analysis

	BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
	PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.
Repeat Finder	All significant local alignments are reported following the full end-to-end self-alignment.
WU-Blast	Do-It-Yourself Sequence Comparison using WU-Blast 2.0
AliBee	Multiple Alignment

Motif Searching

	This program allows to scan a protein sequence (either from Swiss-Prot or TrEMBL or provided by the user) for the occurrence of patterns and profiles stored in the PROSITE database, or to search protein databases with a user-entered pattern
	The MEME/MAST system allows you to discover motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and, search sequence databases using motifs using MAST.
	MOTIF: Searching Protein and Nucleic Acid Sequence Motifs
	PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space.

DNA Primer Design

Primer Design Assistant

RNA Secondary Structure Prediction

The Zuker Group	Algorithms, Thermodynamics and databases for RNA Secondary Structure.
GPRM	Genetic Programming for RNA Motifs
	RNA secondary structure prediction at GeneBee.
RNAsoft	Software for RNA/DNA secondary structure prediction and design
RNAz	RNAz is program for predicting structurally conserved and thermodynamic stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs.
SLASH	The SLASH server finds an appropriate subset of core sequences on your data on which it performs FOLDALIGN to provide a seed alignment used to train a COVE model.
	The applet retrieves the secondary structure from a URL, displays it in a Web page, and responds to user interaction by identifying which objects the user clicked on and optionally calling a URL in response. The applet supports several levels of zooming and uses offscreen imaging for optimized performance.
SSU	SSU rRNA Secondary Structure Prediction and Alignment
Vienna RNA Package	RNA Secondary Structure Prediction and Comparison
XRNA	XRNA is a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams.

RNAi Design

	BD Biosciences Clontech RNAi Designer
	DEQOR, a web-based tool for the Design and Quality Control of siRNAs.
	Dharmacon siRNA Design Center
	GenScript - siRNA Design
BLOCK-iT?	Invitrogen - Block-iT? RNAi Designer
Jack Lin's siRNA sequence finder	Jack Lin's siRNA sequence finder
	QIAGEN uses the most advanced technologies possible for RNAi. The innovative HiPerformance siRNA Design Algorithm and a proprietary homology analysis tool are used for siRNA design (HP siRNA). Patented chemistry is used for siRNA synthesis (HPP Grade siRNA).
	IDT SciTools RNAi Design
	RNAi OligoRetriever
	This tool follows the siRNA design guidelines first described by Tuschl and colleagues. In general, Ambion scientists find that ~50% of siRNAs designed using this tool will reduce target gene expression by >50%.
WI siRNA Selection Program	WI siRNA Selection Program

Microarray Analysis

CONFAC	Conserved Transcription Factor Binding Site Finder
	Data Mining for DNA Microarrays
	Gene Expression Pattern Analysis Suite
MAP	Microarray Annotation and Profile A user-centric bioinformatics environment for microarray data analysis

Biomolecular Interaction

The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature.

Pathway Analysis

ArrayXPath	ArrayXPath is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG)
	BioCarta Pathway Database
	KEGG Pathway Database
	PANTHER Pathway consists of over 107, primarily signaling, pathways, each with subfamilies and protein sequences mapped to individual pathway components. A component is usually a single protein in a given organism, but multiple proteins can sometimes play the same role.

Protein Functional (Domain) Analysis

	Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families.
	ProDom is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases.
	PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs.
	SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable.

Protein Interactions Prediction

	A tool for visualizing the predicted functional associations among genes and proteins in many different organisms.
	ADVICE is a web server providing Automated Detection and Validation of Interaction based on the Co-Evolutions between interacting proteins. It automated the steps needed to compute the similarities between proteins' evolutionary histories to detect co-evolved interacting proteins.
Interaction Prediction	Predicting protein interactions using conserved network motifs in the Saccharomyces Cerevisiae Protein Interaction Map
	Interaction Prediction through Tertiary Structure
	InterDom is a database of putative interacting protein domains derived from multiple sources, ranging from domain fusions (Rosetta Stone), protein interactions (DIP and BIND), protein complexes (PDB), to scientific literature (MEDLINE).
POINT	Prediction Of INTeractome
	STRING - Search Tool for the Retrieval of Interacting Genes/Proteins
	The E Coli Predicted Protein Interactions Database

Protein Secondary Structure Prediction

PSIPRED	PSIPRED is a simple and reliable secondary structure prediction method, incorporating two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST (Position Specific Iterated - BLAST).
HYPROSPII	A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence.
	A consensus method for protein secondary structure prediction
	Network Protein Sequence @nalysis
	Secondary structure and class prediction server
	PredictProtein is an Internet service for sequence analysis and the prediction of protein structure and function. Users submit protein sequences or alignments; PredictProtein returns multiple sequence alignments, PROSITE sequence motifs, low-complexity regions (SEG), nuclear localisation signals, regions lacking regular structure (NORS) and predictions of secondary structure, solvent accessibility, globular regions, transmembrane helices, coiled-coil regions, structural switch regions, disulfide-bonds, sub-cellular localization, and functional annotations.
	YASPIN is a HNN (Hidden Neural Network) secondary structure prediction program that uses the PSI-BLAST algorithm to produce a PSSM for the input sequence, which it then uses to perform its prediction.
PSA	The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence.
Proteus	A universal protein structure prediction server that will take any query protein sequence and predict the secondary structure, membrane spanning helices, membrane spanning beta strands, signal peptides, and 3D structures.

Subcellular Localization Prediction

    Prokaryotic Subcellular Localization Predictors

	PSORT.org provides links to the PSORT family of programs for subcellular localization prediction as well as other datasets and resources relevant to localization prediction. The page is currently hosted by the Brinkman Laboratory at Simon Fraser University, and our goal is to provide an open-source resource centre for researchers interested in subcellular localization prediction.
	a localization prediction tool for Gram-negative bacteria which utilizes support vector machine and PSI-BLAST to generate predictions for 5 localization sites
	This specialized server available at the PENCE Proteome Analyst site is able to classify Gram-negative, Gram-positive, fungi, plant and animal proteins to many localization sites.
	LOCtree is a eukaryotic and prokaryotic localization prediction tool available at the CUBIC site.
CELLO	CELLO uses Support Vector Machine based on n-peptide composition to assign a Gram-negative protein to the cytoplasm, inner membrane, periplasm, outer membrane or extracellular space.
SubLoc	SubLoc uses Support Vector Machine to assign a prokaryotic protein to the cytoplasmic, periplasmic, or extracellular sites, and a eukaryotic protein to the cytoplasmic, mitochondrial, nuclear, or extracellular sites. A modified version of SubLoc was used in PSORT-B v.1.1 to differentiate cytoplasmic and non-cytoplasmic proteins.
SignalP	SingleP predicts traditional N-terminal signal peptides in both prokaryotic and eukaryotic proteins.

    Eukaryotic Subcellular Localization Predictors

	PSORT.org provides links to the PSORT family of programs for subcellular localization prediction as well as other datasets and resources relevant to localization prediction. The page is currently hosted by the Brinkman Laboratory at Simon Fraser University, and our goal is to provide an open-source resource centre for researchers interested in subcellular localization prediction.
pTARGET	pTARGET uses amino acid composition and localization-specific Pfam domains to assign a eukaryotic protein to one of nine localization sites.
pSLIP	pSLIP uses support vector machine and multiple physiochemical properties of amino acids to assign a eukaryotic protein to one of six localization sites.
	HSLPred is a localization prediction tool for human proteins which utilizes support vector machine and PSI-BLAST to generate predictions for 4 localization sites.
	LOCSVMpsi is a eukaryotic localization prediction method that incorporates evolutionary information into its predictions. The method uses PSI-BLAST and support vector machine to generate predictions for up to 12 localization sites.
NucPred	NucPred uses the presence of nuclear localization signals identified through a genetic programming algorithm as the basis of its classification method.
ESLPred	ESLPred uses Support Vector Machine and PSI-BLAST to assign eukaryotic proteins to the nucleus, mitochondrion, cytoplasm, or extracellular space.
	This specialized server available at the PENCE Proteome Analyst site is able to classify Gram-negative, Gram-positive, fungi, plant and animal proteins to many localization sites.
	LOCtree is a eukaryotic and prokaryotic localization prediction tool available at the CUBIC site.
SecretomeP	SecretomeP predicts eukaryotic proteins which are secreted via a non-traditional secretory mechanism.
SignalP	SingleP predicts traditional N-terminal signal peptides in both prokaryotic and eukaryotic proteins.
SubLoc	SubLoc uses Support Vector Machine to assign a prokaryotic protein to the cytoplasmic, periplasmic, or extracellular sites, and a eukaryotic protein to the cytoplasmic, mitochondrial, nuclear, or extracellular sites. A modified version of SubLoc was used in PSORT-B v.1.1 to differentiate cytoplasmic and non-cytoplasmic proteins.
TargetP	TargetP predicts the presence of signal peptides, chloroplast transit peptides, and mitochondrial targeting peptides for plant proteins, and the presence of signal peptides and mitochondrial targeting peptides for eukaryotic proteins.
	PredictNLS uses nuclear localization signal motifs to predict whether a protein might be localized to the nucleus.
	Predotar is designed to predict the presence of mitochondrial and plastid targeting peptides in plant sequences.
couple-subloc	couple-subloc is a prediction system for protein subcellular localization based on amino acid composition alone. Support Vector Machine (SVM) method and k-couple are used in SubLoc couple-subloc predicts locations of prokaryotic and eukaryotic sequences separately.
ProSLP v2.0	ProSLP(Protein Subcellular Localization Prediction) is the system for prediction of subcellular localization. ProSLP performs sequence search by using sequence search method based on n-gram indexing method and predicts information of subcellular location site(s) by using k-NN algorithm.

3D Structure Modelling

	MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints.
SAM	The Sequence Alignment and Modeling system (SAM) is a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis.
SDSC1	SDSC Protein Structure Homology Modeling Server

3D Structure Comparison

	databases and tools for 3D protein structure comparison and alignment using the Combinatorial Extension (CE) Method
	The Dali server is a network service for comparing protein structures in 3D. If you want to know the structural neighbours of a protein already in the Protein Data Bank, you can find them in the FSSP database.
	VAST Search is NCBI's structure-structure similarity search service. It compares 3D coordinates of a newly determined protein structure to those in the MMDB/PDB database. VAST Search computes a list of structure neighbors that you may browse interactively, viewing superpositions and alignments by molecular graphics.
	An advantage of Matras is its structure similarity score, which is defined as the log-odds of the probabilities, similar to Dayhoff's substitution model of amino acids. This score is designed to detect evolutionarily related (homologous) structural similarities.