《核酸研究》.2005年.第We期

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• GPS: a comprehensive www server for phosphorylation sites prediction
• PREDBALB/c: a system for the prediction of peptide binding to H2d mole
• MULTIPRED: a computational system for prediction of promiscuous HLA bi
• GlyProt: in silico glycosylation of proteins
• REPPER—repeats and their periodicities in fibrous proteins
• MEDock: a web server for efficient prediction of ligand binding sites
• DiANNA: a web server for disulfide connectivity prediction
• Fragnostic: walking through protein structure space
• The HHpred interactive server for protein homology detection and struc
• PatMatch: a program for finding patterns in peptide and nucleotide seq
• QuasiMotiFinder: protein annotation by searching for evolutionarily co
• CX, DPX and PRIDE: WWW servers for the analysis and comparison of prot
• H++: a server for estimating pKas and adding missing hydrogens to macr
• BASys: a web server for automated bacterial genome annotation
• CisMols Analyzer: identification of compositionally similar cis-elemen
• nsSNPAnalyzer: identifying disease-associated nonsynonymous single nuc
• EDITORIAL
• Protein structure prediction servers at University College London
• The Diamond STING server
• SOAP-based services provided by the European Bioinformatics Institute
• The Bioinformatics Links Directory: a Compilation of Molecular Biology
• CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational s
• Scooby-domain: prediction of globular domains in protein sequence
• BhairPred: prediction of ?-hairpins in a protein from multiple alignme
• MICheck: a web tool for fast checking of syntactic annotations of bact
• Integrating protein annotation resources through the Distributed Annot
• SNP Cutter: a comprehensive tool for SNP PCR–RFLP assay design
• SNPAnalyzer: a web-based integrated workbench for single-nucleotide po
• Identifying synonymous regulatory elements in vertebrate genomes
• WordSpy: identifying transcription factor binding motifs by building a
• ARTS: a web-based tool for the set-up of high-throughput genome-wide m
• FOOTER: a web tool for finding mammalian DNA regulatory regions using
• AMOD: a morpholino oligonucleotide selection tool
• PriFi: using a multiple alignment of related sequences to find primers
• GENSTYLE: exploration and analysis of DNA sequences with genomic signa
• Assembly PCR oligo maker: a tool for designing oligodeoxynucleotides f
• Stitchprofiles.uio.no: analysis of partly melted DNA conformations usi
• dnaMATE: a consensus melting temperature prediction server for short D
• E-RNAi: a web application to design optimized RNAi constructs
• dsCheck: highly sensitive off-target search software for double-strand
• Kinefold web server for RNA/DNA folding path and structure prediction
• OligoWiz 2.0—integrating sequence feature annotation into the design o
• RACE: Remote Analysis Computation for gene Expression data
• PathwayExplorer: web service for visualizing high-throughput expressio
• MIDAW: a web tool for statistical analysis of microarray data
• ASIAN: a web server for inferring a regulatory network framework from
• WEBSAGE: a web tool for visual analysis of differentially expressed hu
• GenePath: from mutations to genetic networks and back
• GoPubMed: exploring PubMed with the Gene Ontology
• RPBS: a web resource for structural bioinformatics
• SPACE: a suite of tools for protein structure prediction and analysis
• SCRATCH: a protein structure and structural feature prediction server
• PAT: a protein analysis toolkit for integrated biocomputing on the web
• Dcode.org anthology of comparative genomic tools
• Fragment Finder: a web-based software to identify similar three-dimens
• ProTarget: automatic prediction of protein structure novelty
• PROTINFO: new algorithms for enhanced protein structure predictions
• LOCSVMPSI: a web server for subcellular localization of eukaryotic pro
• WebProAnalyst: an interactive tool for analysis of quantitative struct
• PISCES: recent improvements to a PDB sequence culling server
• ProFunc: a server for predicting protein function from 3D structure
• PhyloDome—visualization of taxonomic distributions of domains occurrin
• InterProScan: protein domains identifier
• AS2TS system for protein structure modeling and analysis
• pdbFun: mass selection and fast comparison of annotated PDB residues
• DIAL: a web-based server for the automatic identification of structura
• PRODOC: a resource for the comparison of tethered protein domain archi
• GRIFFIN: a system for predicting GPCR–G-protein coupling selectivity u
• GPCRsclass: a web tool for the classification of amine type of G-prote
• PEPVAC: a web server for multi-epitope vaccine development based on th
• TMBETA-NET: discrimination and prediction of membrane spanning ?-stran
• CEP: a conformational epitope prediction server
• TRAMPLE: the transmembrane protein labelling environment
• Web-based toolkits for topology prediction of transmembrane helical pr
• TMB-Hunt: a web server to screen sequence sets for transmembrane ?-bar
• GraBCas: a bioinformatics tool for score-based prediction of Caspase-
• Pcleavage: an SVM based method for prediction of constitutive proteaso
• KinasePhos: a web tool for identifying protein kinase-specific phospho
• SEARCHGTr: a program for analysis of glycosyltransferases involved in
• ProTeus: identifying signatures in protein termini
• SCANMOT: searching for similar sequences using a simultaneous scan of
• SVC: structured visualization of evolutionary sequence conservation
• MINER: software for phylogenetic motif identification
• PRALINE: a multiple sequence alignment toolbox that integrates homolog
• FFAS03: a server for profile–profile sequence alignments
• One-Block CYRCA: an automated procedure for identifying multiple-block
• SRide: a server for identifying stabilizing residues in proteins
• ConSurf 2005: the projection of evolutionary conservation scores of re
• Manipulating multiple sequence alignments via MaM and WebMaM
• MAVL/StickWRLD for protein: visualizing protein sequence families to d
• I-Mutant2.0: predicting stability changes upon mutation from the prote
• MutDB services: interactive structural analysis of mutation data
• GEPAS, an experiment-oriented pipeline for the analysis of microarray
• ArrayXPath II: mapping and visualizing microarray gene-expression data
• VAMPIRE microarray suite: a web-based platform for the interpretation
• ASePCR: alternative splicing electronic RT–PCR in multiple tissues and
• OrfPredictor: predicting protein-coding regions in EST-derived sequenc
• miRU: an automated plant miRNA target prediction server
• MicroInspector: a web tool for detection of miRNA binding sites in an
• GFINDer: genetic disease and phenotype location statistical analysis a
• BRIGEP—the BRIDGE-based genome–transcriptome–proteome browser
• AISMIG—an interactive server-side molecule image generator
• The multilocus sequence typing network: mlst.net
• The bioinformatics resource for oral pathogens
• WebGestalt: an integrated system for exploring gene sets in various bi
• Data mining tools for the Saccharomyces cerevisiae morphological datab
• GeneSeeker: extraction and integration of human disease-related inform
• Recent additions and improvements to the Onto-Tools
• MRS: a fast and compact retrieval system for biological data
• Current Comparative Table(CCT) automates customized searches of dynam
• T-STAG: resource and web-interface for tissue-specific transcripts and
• The FOLDALIGN web server for pairwise structural RNA alignment and mut
• AntiHunter 2.0: increased speed and sensitivity in searching BLAST out
• GBA server: EST-based digital gene expression profiling
• TargetIdentifier: a webserver for identifying full-length cDNAs from E
• RibEx: a web server for locating riboswitches and other conserved bact
• The tRNAscan-SE, snoscan and snoGPS web servers for the detection of t
• éclair—a web service for unravelling species origin of sequences sampl
• PubFinder: a tool for improving retrieval rate of relevant PubMed abst
• LitMiner and WikiGene: identifying problem-related key players of gene
• BIOVERSE: enhancements to the framework for structural, functional and
• PPG: online generation of protein pictures and animations
• SiteEngines: recognition and comparison of binding sites and protein–p
• PRISM: protein interactions by structural matching
• Metabolic PathFinding: inferring relevant pathways in biochemical netw
• VisANT: data-integrating visual framework for biological networks and
• EVAcon: a protein contact prediction evaluation service
• POPSCOMP: an automated interaction analysis of biomolecular complexes
• PatchDock and SymmDock: servers for rigid and symmetric docking
• MovieMaker: a web server for rapid rendering of protein motions and in
• The FoldX web server: an online force field
• DeNovoID: a web-based tool for identifying peptides from sequence and
• PCE: web tools to compute protein continuum electrostatics
• AthaMap web tools for database-assisted identification of combinatoria
• TOUCAN 2: the all-inclusive open source workbench for regulatory seque
• enoLOGOS: a versatile web tool for energy normalized sequence logos
• AUGUSTUS: a web server for gene prediction in eukaryotes that allows u
• BABELOMICS: a suite of web tools for functional annotation and analysi
• SNPServer: a real-time SNP discovery tool
• PromoterPlot: a graphical display of promoter similarities by pattern
• ARGO: a web system for the detection of degenerate motifs and large-sc
• POCO: discovery of regulatory patterns from promoters of oppositely ex
• P-Match: transcription factor binding site search by combining pattern
• T-Reg Comparator: an analysis tool for the comparison of position weig
• CONREAL web server: identification and visualization of conserved tran
• GeneMark: web software for gene finding in prokaryotes, eukaryotes and
• Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC
• JCat: a novel tool to adapt codon usage of a target gene to its potent
• YASS: enhancing the sensitivity of DNA similarity search
• PARALIGN: rapid and sensitive sequence similarity searches powered by
• MuPlex: multi-objective multiplex PCR assay design
• POWER: PhylOgenetic WEb Repeater—an integrated and user-optimized fram
• SOP3v2: web-based selection of oligonucleotide primer trios for genoty
• FeatureExtract—extraction of sequence annotation made easy
• Projector 2: contig mapping for efficient gap-closure of prokaryotic g
• PHYML Online—a web server for fast maximum likelihood-based phylogenet
• DINAMelt web server for nucleic acid melting prediction
• GEMS: a web server for biclustering analysis of expression data
• T-profiler: scoring the activity of predefined groups of genes using g
• RNALOSS: a web server for RNA locally optimal secondary structures