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R & D          
The Sub Distribution Information Centre of JNTBGRI under the Biotechnology Information System Network is providing access to popular resources on Bioinformatics.
Open Source Databases
Protein Information Resource (P I R)  
The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information.
National Center for Biotechnology Information (NCBR)  
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
TSIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.
EMBL - European Bioinformatics Institute(EBI)  
EMBL-EBI is a centre for research and services in bioinformatics. It has diversified to provide data resources in all the major molecular domains and expanded to include a broad research base. It provides user support and offers advanced training in bioinformatics.
Protein Data Bank (P D B)  
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.
Protein Data Bank Japan(P D B j)  
PDBj maintains the database for the protein structures collaborating with RCSB, PDBe and BMRB
Protein Data Bank Europe(P D B e)  
A European resource for PDB protein structure deposition and PDB structure annotation to the wwPDB.
BMRB - Biological Magnetic Resonance Bank  
Database for NMR spectroscopy information on biomolecules.
GMOD - Generic Model Organism Database  
Collection of open source software tools for creating and managing genome-scale biological databases.
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
ICGEB - International Centre for Genetic Engineering and Biotechnology  
An International centre for genetic engineering and Biotechnology. With special regard to the needs of the developing world.
A non-redundant composite of 4 publicly-available primary sources: SWISSPROT, PIR (1-3), GenBank (translation) and NRL-3D.
CATH is a manually curated classification of protein domain structures.
SCOP - Structural Classification of Proteins  
Detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.
PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterize a protein family
First secondary database of proteins and motifs are encoded as regular expressions, often simply referred to as patterns.
Multiple-motif database, based on protein families contained in PROSITE database.
Pfam - Protein Family  
A database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.
A database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.
ProDom - Protein domain  
ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.
Global bioinformatic directory
KEGG - Kyoto Encyclopedia of Genes and Genomes  
A bioinformatics resource for linking genomes to life and the environment. This database is a collection of online databases, dealing with genomes, enzymatic pathways and biological chemicals.
PANTHER - Protein ANalysis THrough Evolutionary Relationships  
A database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.
BioCyc is a collection of 1690 Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism.
MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways.
INOH - Integrating Network Objects with Hierarchies  
Metabolic pathway database.
PathCase - Pathways Database System  
Each PathCase application contains a different set of tools. All applications store, query, and visualize metabolic pathways, in addition to their specialized tasks.
MMMDB - Mouse Multiple Tissue Metabolome Database  
Provides comprehensive and quantitative metabolomic information for multiple tissues from single mice.
EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.
An openfree web resource and encyclopedia of world wide SNP (Single Nucleotide Polymorphism) researchers and supports the international genome variance researches by collecting, organizing, analyzing, and disseminating variome information.
HapMap - Haplotype Map  
Public resource that will help researchers find genes associated with human disease and response to pharmaceuticals.
DDBJ - DNA Data Bank of Japan  
DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.
The Gene Ontology  
Standardizing the representation of gene and gene product attributes across species and databases.
The Eukaryotic Promoter Database  
An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.
An extensive relational database schema and associated application framework designed to store, integrate, analyze and present functional genomics data.
GeneCards is a searchable, integrated, database of human genes that provides concise genomic related information, on all known and predicted human genes.
Sanger Institute  
A leader genome research institute in the Human Genome Project, now focused on understanding the role of genetics in health and disease
The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
AceDB is a database designed specifically for handling genome and bioinformatic data.AceDB was originally developed for the C.elegans genome project. However, the tools in it have been generalized to be much more flexible and the same software is now used for many different genomic databases from bacteria to fungi to plants to man. It is also increasingly used for databases with non-biological content.
A searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation.
This browser provides the latest sequence and annotation of the Zea mays ssp. mays genome resulting from the Maize Genome Sequencing Project. The browser is based on the AGI Agarose FPC Map and on BAC clone sequences contained therein. Sequencing of the B73 cultivar commenced in November 2005 as part of a 3-year multi-institutional collaboration funded jointly by the NSF, USDA and DOE. The strategy is to individually sequence a set BAC clones across a minimal-tiling path. Gene space will be identified and sequenced to finished quality. As of February 27, 2008, the consortium completed the draft sequence of the maize genome and will improve the sequence through the end of 2008.
HIV Sequence database  
The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials.
RDP - Ribosomal DataBase Project  
The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community, including online data analysis and aligned and annotated Bacterial and Archaeal small-subunit 16S rRNA sequences.
SiRNA databases and resources for RNA interference studies  
The discovery of reagents to inhibit RNA synthesis and translation has revolutionized the study of biological processes. These tools include small inhibitory RNA (siRNA), small hairpin RNA (shRNA) and ribozymes.
Gramene is a curated, open-source, data resource for comparative genome analysis in the grasses. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations.
Allen Institute of Brain science  
A growing collection of online public resources integrating extensive gene expression and neuroanatomical data, complete with a novel suite of search and viewing tools.
SGD - Saccharomyces Genome Database  
A scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.
PomBase - Pombe Database  
PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.
1001 genomes  
The 1001 Genomes Project, launched at the beginning of 2008, has as a goal to discover the whole-genome sequence variation in 1001 strains (accessions) of the reference plant Arabidopsis thaliana. The resulting information is paving the way for a new era of genetics that identifies alleles underpinning phenotypic diversity across the entire genome and the entire species.
TAIR - The Arabidopsis Information Resource  
Maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana
MaizeGDB - Maize Genome DataBase  
MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays.
New and more biologically meaningful organization of the genomic data presented on GBrowse for D. melanogaster.
WormBase at Caltech (at Pasadena, CA, USA) currently has seven full-time biological curators as well as several bioinformaticians and software developers. The Caltech group annotates gene expression patterns, gene regulation, functional descriptions, phenotypes, microarray data, cell functions, and protein and gene interactions. We continually try to obtain, store and display whatever information has become most relevant to our community.
ZFIN - The Zebrafish Information Network  
Zebra fish organism model database.
MGI - Mouse Genome Informatics  
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease
RGD - Rat Genome Database  
Excellent source of information about rat strains and their associated physiology, phenotypes and diseases.
SCOR - Structural Classification of RNA  
Designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships.
Noncoding RNA database  
The noncoding RNA (ncRNA) database is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Currently, the database includes over 30,000 individual sequences from 99 species of Bacteria, Archaea and Eukaryota.
miRBase - Micro RNA sequences dataBase  
Database of published miRNA sequences and annotation.
TissueInfo is a program that determines the tissue expression profile of a sequence.
Nucleic acid database  
A repository of three-dimensional structural information about nucleic acids.
The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains 6707 drug entries including 1436 FDA-approved small molecule drugs, 134 FDA-approved biotech (protein/peptide) drugs, 83 nutraceuticals and 5086 experimental drugs. Additionally, 4228 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 150 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.
Therapeutic Target Database  
A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status.
PharmGKB - The Pharmacogenomics Knowledge Base  
Pharmacogenomic knowledge database. An extensive web resource for analyzing 332828 drug-target interactions.
SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.
NCBI - National Centre for Biotechnology Information  
Provide tools to analyze biological data using NCBI software
EMBL-EBI - European Molecular Biology Laboratory-European Bioinformatics Institute  
EMBL-EBI is a centre for research and services in bioinformatics. It has diversified to provide data resources in all the major molecular domains and expanded to include a broad research base. It provides user support and offers advanced training in bioinformatics.
Gene Locator and Interpolated Markov ModelER/ Gene Locator and Interpolated Markov ModelER Hidden Markov Model
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
GeneZilla is a state-of-the-art gene finder based on the Generalized Hidden Markov Model framework, similar to Genscan and Genie. It is highly reconfigurable and includes software for retraining by the end-user. It is written in highly optimized C++. The run time and memory requirements are linear in the sequence length, and are in general much better than those of competing systems, due to GeneZilla's novel decoding algorithm. Graph-theoretic representations of the high scoring open reading frames are provided, allowing for exploration of sub-optimal gene models. It utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, CAP sites, and will soon model CpG islands as well.
Identification of complete gene structures of a genomic DNA.
ORFFinder - Open Readomg Frame Finder  
This web page is designed to align a mRNA sequence to a genomic sequence to find the exons in a gene. The two sequence must be from the same species and so highly homolgous for the common regions. If an open reading frame is selected that too is included in the alignment.
A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.
It provides co-regulates gene relations to estimate gene function.
This WEB tool helps to assign structural domains to protein sequences and to classify them according to SCOP.
Domain prediction tool.
DSSP - Database of Secondary Structure Assignments  
The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).
Target Optimisation Utility  
TarO analyses a protein sequence by a large number of bioinformatics techniques. These include crystallisation propensity prediction, orthologue searching, and many other sequence based calculations.
A framework and web portal specifically aimed at the integration of bioinformatics software and databanks.
PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein and protein-DNA binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges.
FunClust is a web server for the identification of local functional motifs in a set of non homologous protein structures.
SABLE - Solvent AccessiBiLitiEs  
SABLE server can be used for prediction of the protein secondary structure, relative solvent accessibility and trans-membrane domains.
DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone.
DiANNA is a recent state-of-the-art artificial neural network and web server, which determines the cysteine oxidation state and disulfide connectivity of a protein, given only its amino acid sequence.
Disulfide by Design  
Disulfide by Design is an application for the rational design of disulfide bonds in proteins.
CYSREDOX - REDOX state of CYSteins  
Predicting redox state of cysteins in proteins from multiple sequence alignment.
DSDBASE - DiSulphide DataBASE  
DSDBASE is a database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein.
A dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker.
Bioinformatics Toolkit  
Collection of tertiary structure prediction tools.
Fully automated protein structure homology-modeling server.
ESyPred3D- Expert System for the Prediction of proteins 3D structures  
ESyPred3D is a new automated homology modeling program.
This server builds three-dimensional models for proteins based on homologues of known structure.
CASP - the Critical Assessment of protein Structure Prediction  
The Critical Assessment of protein Structure Prediction (CASP) experiments aim at establishing the current state of the art in protein structure prediction, identifying what progress has been made, and highlighting where future effort may be most productively focused.
CPHmodels 3.0 is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions.
Combines sequence and structural information for predicting the structure and/or function of protein sequence.
LOOPP is a fold recognition program based on the collection of numerous signals, merging them into a single score, and generating atomic coordinates based on an alignment into a homologue template structure.
DALI server  
The Dali server is a network service for comparing protein structures in 3D.
RASMOT-3D PRO searches in protein structure files for proteins possessing a group of residues in a topology similar to that adopted by a 3D motif given in input.
A server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure.
A versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.
I-TASSER server is an Internet service for protein structure and function predictions.
Protein sequence conservation can be a valuable tool to assess functional regions of a protein.
Analysis of functional relationships in protein families as inferred from protein surface maps comparison.
Molecular surface of proteins with the electrostatic potential is a representation of protein three dimensional structures, which often gives some clues to infer the function of proteins.
Programs that assess structural similarity compare two structures to each other and define common regions.
Predicts functionally important residues. Predictions are made by evaluating internally generated alignments using SQUARE.
The tool is meant for binding sites and active sites of proteins and DNAs are often associated with structural pockets and cavities.
Qsite Finder  
The tool is meant for binding sites and active sites of proteins and DNAs are often associated with structural pockets and cavities.
Qsite Finder  
Prediction of biomolecular interaction sites and protein function.
Prediction of ligand binding site.
Identification and evaluation of surface binding-pockets and occluded cavities are initial steps in protein structure-based drug design.
FINDSITE is a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures.
For a given protein sequence or structure query, IBIS reports physical interactions observed in experimentally-determined structures for this protein. IBIS also infers/predicts interacting partners and binding sites by homology, by inspecting the protein complexes formed by close homologs of a given query. To ensure biological relevance of inferred binding sites, the IBIS algorithm clusters binding sites formed by homologs based on binding site sequence and structure conservation.
3D-SURFER is web-based software for protein surface comparison and analysis. The server integrates various repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons. It takes less than a second to perform an exhaustive comparison between a single protein surface to all protein structures in the current PDB.
Ligand coordinates are used to demarcate the binding site.
ConSurf Server  
The server for the Identification of Functional Regions in Proteins.
MetalDetector predicts metal binding sites in proteins using sequence information alone. Prediction is limited to transition metals (with the addition of heme and Fe/S clusters) and to CYS and HIS as ligands. In this release, MetalDetector predicts the number of bound metal ions and, for each ion, CYS and HIS ligands in the sequence.
A web server for generating 3D protein structures using NOE-derived distance restraints and NMR chemical shifts.
Catalytic Site Atlas  
Documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
Protein Peeling v2  
An approach for splitting a 3D protein structure into proteins units.
pDomain resource is centered around defining structural domains from 3D coordinates.
Prediction of domains.
DIAL is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.
Intrinsic protein disorder, domain and globularity prediction.
PURE is a bioinformatics protocol to identify putative domains in the Unassigned Regions[UR]. PURE is now available as a web server. Users can submit the sequence of unassigned regions or linker regions to predict domains encoded in them.
Domain 3D  
Domain 3D is a method developed by Willie Taylor to identify globular domains in protein structure.
TLS Motion Determination  
TLS Motion Determination (TLSMD) analyzes a macromolecular crystal structure for evidence of flexibility, e.g. local or inter-domain motions. It does this by partitioning individual chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion. It generates all possible partitions up to a maximum number of segments.
CAVER is a software tool for analysis and visualisation of tunnels and channels in protein structures. Tunnels are void pathways leading from a cavity buried in a protein core to the surrounding solvent. Unlike tunnels, channels lead through the protein structure and their both endings are opened to the surrounding solvent. Studying of these pathways is highly important for drug design and molecular enzymology.
HotPatch Web Gateway  
HotPatch finds unusual patches on the surface of proteins, and computes just how unusual they are (patch rareness), and how likely each patch is to be of functional importance (functional confidence (FC).) The statistical analysis is done by comparing your protein's surface against the surfaces of a large set of proteins whose functional sites are known.
MolLoc is a web server for the comparison of molecular surfaces such as binding sites, cavities and any residue selection.
PLATINUM is designed for calculation of hydrophobic properties of molecules and their match or mismatch in receptor-ligand complexes.
PINTS finds reoccuring three-dimensional patterns of amino acids. These amino-acids are close in space but not necessarily close or co-linear in sequence, for example the serine-protease catalytic triad. Unlike other tools, PINTS does not aim to find proteins adopting a similar fold.
DynDom is a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.
FLEXWEB is the FRODA module (Framework Rigidity Optimized Dynamics Algorithm) which moves the static results of a FIRST6 analysis into the realm of dynamics where we actually explore the conformational space available to flexible regions.
An algorithm for protein hinge prediction using elastic network models.
Recognizes spatial chemical binding patterns common to a set of protein structures.
Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation -? interactions within a protein or between proteins in a complex.
STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.
This web site analyzes structure of proteins and output the list of hydrogen bonding patterns network motifs. The list of motifs, a superset of the secondary structures, is shown both projected on the protein structure and as a network motif significance profile (SP), a chart which gives the occurrences of each motif in the protein.
Quite often a biomolecular researcher wants to quickly calculate solvent accessible surface area or solvation energy.
ASAP predicts solvent accessible surface area of proteins. Currently the Web predictor only accepts single protein sequence as input. Please select the type of protein and enter protein sequence in FASTA format in the text area.
The Rensselaer Exploratory Center for Cheminformatics Research is dedicated to advancing the field of Cheminformatics and increasing the availability of new methods within the Cheminformatics user community.
This PIPSA service is provided for the comparison of the electrostatic interaction properties of proteins. It permits the classification of proteins according to their interaction properties. PIPSA may assist in function assignment, the estimation of binding properties and enzyme kinetic parameters.
Recognizes spatially conserved chemical interactions shared by a set of PPIs.
121-Site Engine  
Surface and physico-chemical alignment of proteinprotein interfaces.
MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures.
AquaProt analyses protein-protein binding interface, defines inter-residue interaction map within the interface and extracts related water molecules.
VASCo is a program pipeline including a visualization tool to calculate and visualize annotated surfaces with special emphasis on surface contact regions and protein-protein interactions. Crystal contacts and biological contacts can be calculated based on surface points. Molecular properties such as electrostatic potential or hydrophobicity can be calculated and mapped on those surface points. The molecular surfaces and properties are calculated using existing established programs, which are integrated into the package, as well as using own developed programs. The modular pipeline can easily be extended to include new properties for annotation. The output of this pipeline is most conveniently displayed in PyMOL as Compiled Graphics Objects (CGO) using a custom-made plug-in.
SPPIDER is a server for identification of residues involved in protein-protein interactions.
FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.
SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations.
CUPSAT is a tool to predict changes in protein stability upon point mutations. The prediction model uses amino acid-atom potentials and torsion angle distribution to assess the amino acid environment of the mutation site. Additionally, the prediction model can distinguish the amino acid environment using its solvent accessibility and secondary structure specificity.
Prediction of Protein Stability Changes for Single-Site Mutations from Sequences.
Estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein.
ConSurf Server  
A server for identification of conserved regions in nucleotides.
The focus of the DIANA lab is on the development of algorithms, databases and tools for interpreting and archiving genomic data in the framework of a systemic analysis. Current emphasis is on the analysis of microRNA (miRNA) and protein coding genes. MiRNAs are recently identified to be very abundant in mammalian organisms and play a key role in regulating development.
ORF Finder  
The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. This tool identifies all open reading frames using the standard or alternative genetic codes.
Webcutter is a useful tool for experimentors working with recombinant DNA.
The tool screens DNA sequences in FASTA format against a library of repetitive elements and returns a masked query sequence ready for database searches. RepeatMasker also generates a table annotating the masked regions.
Scientific databases and tools
Tools and databases
Databases of immunoinformatics
Metabolomics society  
Metabolic databases.
Dot Matrix Plot  
Dot or matrix plots provide an easy and powerful means of sequence analysis, useful for searching out regions of similarity in two sequences and repeats within a single sequence.
LALIGN find internal duplications by calculating non-intersecting local alignments of protein or DNA sequences.
SIM4 addresses the problem of efficiently aligning a transcribed and spliced DNA sequence (mRNA, EST) with a genomic sequence containing that gene, allowing for introns in the genomic sequence (taking into account consensus splice signals) and a relatively small number of sequencing errors.
DNA and protein sequence alignment software package
RNAfold web server  
The RNAfold web server will predict secondary structures of single stranded RNA or DNA sequences.
A free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
Multiple sequence alignment tool.
Generates sequence logos, graphical representations of the patterns within a multiple sequence alignment.
T-ACE was developed for the analysis and organization of transcriptome projects but is also helpful for the organization of small sequence datasets e.g. extracts of a large transcriptome databases.
PAUP version 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees, for use in Macintosh, Windows, UNIX / VMS, or DOS-based formats. The influence of high-speed computer analysis of molecular, morphological and/or behavioral data to inter phylogenetic relationships has expanded well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse as conservation biology, ecology, and forensic studies.
A free computational phylogenetics package of programs for inferring evolutionary trees.
For drawing phylogenetic trees.
Software package for extensive data analysis in molecular biology and evolution, for Windows ME/2000/XP/VISTA and Linux.
Package that performs molecular phylogenetic inference.
A program for building and displaying phylogenetic trees of protein and nucleic acid sequences.
Jevtrace is a Java implementation of the evolutionary trace method.
NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
IMGT web resources  
The IMGT Immunoinformatics page comprises links to databases, tools and resources on immunoglobulins (IG) or antibodies, T cell receptors (TR) and major histocompatibility complex (MHC).
A yeast phenome database.
An established portal that allow phenome data to be collectively searched for phenotypes and associated information.
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