* Detection of reliable and unexpected protein fold predictions using 3D-Jury * DSSPcont: continuous secondary structure assignments for proteins * PROTINFO: secondary and tertiary protein structure prediction * The PredictProtein server * GeneSilico protein structure prediction meta-server * META-PP: single interface to crucial prediction servers * EVA: evaluation of protein structure prediction servers * VADAR: a web server for quantitative evaluation of protein structure quality * ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins * WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures * 3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs * Motif3D: relating protein sequence motifs to 3D structure * LOC3D: annotate sub-cellular localization for protein structures * Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures * NCI: a server to identify non-canonical interactions in protein structures * MolSurfer: a macromolecular interface navigator * CASTp: Computed Atlas of Surface Topography of proteins * SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules * Servers for sequence–structure relationship analysis and prediction * POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level * MATRAS: a program for protein 3D structure comparison * LGA: a method for finding 3D similarities in protein structures * Tools for comparative protein structure modeling and analysis * SWISS-MODEL: an automated protein homology-modeling server * STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence * Integrated databanks access and sequence/structure analysis services at the PBIL * NRSAS: Nuclear Receptor Structure Analysis Servers * SSEP: secondary structural elements of proteins * Mfold web server for nucleic acid folding and hybridization prediction * RNAsoft: a suite of RNA secondary structure prediction and design software tools * Pfold: RNA secondary structure prediction using stochastic context-free grammars * Vienna RNA secondary structure server * PseudoViewer2: visualization of RNA pseudoknots of any type * A software tool-box for analysis of regulatory RNA elements * GPRM: a genetic programming approach to finding common RNA secondary structure elements * Tools for the automatic identification and classification of RNA base pairs * GEPAS: a web-based resource for microarray gene expression data analysis * INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis * GenePublisher: automated analysis of DNA microarray data * ExpressYourself: a modular platform for processing and visualizing microarray data * ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis * REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data * Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays * Multiple sequence alignment with the Clustal series of programs * CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics * Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments * SLAM web server for comparative gene finding and alignment * Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence * MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences * MAVID multiple alignment server * EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae * MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences * RevTrans: multiple alignment of coding DNA from aligned amino acid sequences * PromH: promoters identification using orthologous genomic sequences * FIE2: a program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes * PromoSer: a large-scale mammalian promoter and transcription start site identification service * Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes * ETOPE: evolutionary test of predicted exons * ESEfinder: a web resource to identify exonic splicing enhancers * SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences * MATCHTM: a tool for searching transcription factor binding sites in DNA sequences * Gibbs Recursive Sampler: finding transcription factor binding sites * YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation * Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors * Regulatory Sequence Analysis Tools * GeneSeqer@PlantGDB: gene structure prediction in plant genomes * GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders * Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes * PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences * PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria * Signal search analysis server * MHCPred: a server for quantitative prediction of peptide–MHC binding * ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins * Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-{Pi}, NMT and PTS1 * Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs * Static benchmarking of membrane helix predictions * The web server of IBM's Bioinformatics and Pattern Discovery group * Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN * SEARCHPKS: a program for detection and analysis of polyketide synthase domains * MAK, a computational tool kit for automated MITE analysis * Cluster-Buster: finding dense clusters of motifs in DNA sequences * SIC: a tool to detect short inverted segments in a biological sequence * mreps: efficient and flexible detection of tandem repeats in DNA * SPA: simple web tool to assess statistical significance of DNA patterns * TRACTS: a program to map oligopurine.oligopyrimidine and other binary DNA tracts * DNA analysis servers: plot.it, bend.it, model.it and IS * NEBcutter: a program to cleave DNA with restriction enzymes * SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence * BPROMPT: a consensus server for membrane protein prediction * GlobPlot: exploring protein sequences for globularity and disorder * iSPOT: a web tool to infer the interaction specificity of families of protein modules * Automated Gene Ontology annotation for anonymous sequence data * ESTAnnotator: a tool for high throughput EST annotation * Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes * AMIGene: Annotation of MIcrobial Genes * AHMII: Agent to Help Microbial Information Integration * DNannotator: annotation software tool kit for regional genomic sequences * Bioverse: functional, structural and contextual annotation of proteins and proteomes * FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences * EuGEne'Hom: a generic similarity-based gene finder using multiple homologous sequences * PROBEmer: a web-based software tool for selecting optimal DNA oligos * Primer Design Assistant (PDA): a web-based primer design tool * DePIE: Designing Primers for Protein Interaction Experiments * OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling * CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design * RNA-related tools on the Bielefeld Bioinformatics Server * SIRW: a web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches * Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate * Swiss EMBnet node web server * ExPASy: the proteomics server for in-depth protein knowledge and analysis * UniqueProt: creating representative protein sequence sets * BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases * WU-Blast2 server at the European Bioinformatics Institute * OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms * ORFeus: detection of distant homology using sequence profiles and predicted secondary structure * ParseSNP: a tool for the analysis of nucleotide polymorphisms * SIFT: predicting amino acid changes that affect protein function * ActionMap: a web-based software that automates loci assignments to framework maps * WEB-THERMODYN: sequence analysis software for profiling DNA helical stability * NEWT, a new taxonomy portal * Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription * PipeAlign: a new toolkit for protein family analysis * NORSp: predictions of long regions without regular secondary structure * Biological SOAP servers and web services provided by the public sequence data bank * FootPrinter: a program designed for phylogenetic footprinting * GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives * Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes * Building protein diagrams on the web with the residue-based diagram editor RbDe * CRP: Cleavage of Radiolabeled Phosphoproteins * JVirGel: calculation of virtual two-dimensional protein gels * Update on XplorMed: a web server for exploring scientific literature