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《核酸研究医学期刊》2005年第13期

the bioinformatics links directory: a compilation of molecular biology web servers
soap-based services provided by the european bioinformatics institute
the diamond sting server
protein structure prediction servers at university college london
space: a suite of tools for protein structure prediction and analysis based on complementarity and environment
rpbs: a web resource for structural bioinformatics
campo, scr_find and chc_find: a suite of web tools for computational structural biology
dcode.org anthology of comparative genomic tools
pat: a protein analysis toolkit for integrated biocomputing on the web
scratch: a protein structure and structural feature prediction server
protinfo: new algorithms for enhanced protein structure predictions
protarget: automatic prediction of protein structure novelty
fragment finder: a web-based software to identify similar three-dimensional structural motif
profunc: a server for predicting protein function from 3d structure
pisces: recent improvements to a pdb sequence culling server
webproanalyst: an interactive tool for analysis of quantitative structure
locsvmpsi: a web server for subcellular localization of eukaryotic proteins using svm and profile of psi-blast
as2ts system for protein structure modeling and analysis
interproscan: protein domains identifier
phylodome―visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets
prodoc: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families
dial: a web-based server for the automatic identification of structural domains in proteins
pdbfun: mass selection and fast comparison of annotated pdb residues
pepvac: a web server for multi-epitope vaccine development based on the prediction of supertypic mhc ligands
gpcrsclass: a web tool for the classification of amine type of g-protein-coupled receptors
griffin: a system for predicting gpcr
bhairpred: prediction of ?-hairpins in a protein from multiple alignment information using ann and svm techniques
scooby-domain: prediction of globular domains in protein sequence
tmbeta-net: discrimination and prediction of membrane spanning ?-strands in outer membrane proteins
cep: a conformational epitope prediction server
multipred: a computational system for prediction of promiscuous hla binding peptides
predbalb/c: a system for the prediction of peptide binding to h2d molecules, a haplotype of the balb/c mouse
gps: a comprehensive www server for phosphorylation sites prediction
tmb-hunt: a web server to screen sequence sets for transmembrane ?-barrel proteins
web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and compara..
trample: the transmembrane protein labelling environment
pcleavage: an svm based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences
grabcas: a bioinformatics tool for score-based prediction of caspase- and granzyme b-cleavage sites in protein sequences
glyprot: in silico glycosylation of proteins
searchgtr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites
kinasephos: a web tool for identifying protein kinase-specific phosphorylation sites
dianna: a web server for disulfide connectivity prediction
medock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm
repper―repeats and their periodicities in fibrous proteins
the hhpred interactive server for protein homology detection and structure prediction
fragnostic: walking through protein structure space
cx, dpx and pride: www servers for the analysis and comparison of protein 3d structures
quasimotifinder: protein annotation by searching for evolutionarily conserved motif-like patterns
patmatch: a program for finding patterns in peptide and nucleotide sequences
miner: software for phylogenetic motif identification
svc: structured visualization of evolutionary sequence conservation
scanmot: searching for similar sequences using a simultaneous scan of multiple sequence motifs
proteus: identifying signatures in protein termini
one-block cyrca: an automated procedure for identifying multiple-block alignments from single block queries
ffas03: a server for profile
praline: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
manipulating multiple sequence alignments via mam and webmam
consurf 2005: the projection of evolutionary conservation scores of residues on protein structures
sride: a server for identifying stabilizing residues in proteins
i-mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
mavl/stickwrld for protein: visualizing protein sequence families to detect non-consensus features
mutdb services: interactive structural analysis of mutation data
ppg: online generation of protein pictures and animations
bioverse: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes
metabolic pathfinding: inferring relevant pathways in biochemical networks
prism: protein interactions by structural matching
siteengines: recognition and comparison of binding sites and protein
popscomp: an automated interaction analysis of biomolecular complexes
evacon: a protein contact prediction evaluation service
visant: data-integrating visual framework for biological networks and modules
moviemaker: a web server for rapid rendering of protein motions and interactions
patchdock and symmdock: servers for rigid and symmetric docking
h++: a server for estimating pkas and adding missing hydrogens to macromolecules
pce: web tools to compute protein continuum electrostatics
denovoid: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy
the foldx web server: an online force field
enologos: a versatile web tool for energy normalized sequence logos
toucan 2: the all-inclusive open source workbench for regulatory sequence analysis
athamap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sit..
cismols analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes
basys: a web server for automated bacterial genome annotation
babelomics: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments
augustus: a web server for gene prediction in eukaryotes that allows user-defined constraints
integrating protein annotation resources through the distributed annotation system
micheck: a web tool for fast checking of syntactic annotations of bacterial genomes
nssnpanalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms
identifying synonymous regulatory elements in vertebrate genomes
snpanalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis
snp cutter: a comprehensive tool for snp pcr
snpserver: a real-time snp discovery tool
arts: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the snp genotyping of mouse mutants
wordspy: identifying transcription factor binding motifs by building a dictionary and learning a grammar
argo: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters
promoterplot: a graphical display of promoter similarities by pattern recognition
poco: discovery of regulatory patterns from promoters of oppositely expressed gene sets
p-match: transcription factor binding site search by combining patterns and weight matrices
t-reg comparator: an analysis tool for the comparison of position weight matrices
footer: a web tool for finding mammalian dna regulatory regions using phylogenetic footprinting
conreal web server: identification and visualization of conserved transcription factor binding sites
genemark: web software for gene finding in prokaryotes, eukaryotes and viruses
amod: a morpholino oligonucleotide selection tool
genstyle: exploration and analysis of dna sequences with genomic signature
prifi: using a multiple alignment of related sequences to find primers for amplification of homologs
assembly pcr oligo maker: a tool for designing oligodeoxynucleotides for constructing long dna molecules for rna production
jcat: a novel tool to adapt codon usage of a target gene to its potential expression host
multiple alignment of genomic sequences using chaos, dialign and abc
paralign: rapid and sensitive sequence similarity searches powered by parallel computing technology
yass: enhancing the sensitivity of dna similarity search
muplex: multi-objective multiplex pcr assay design
sop3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms
power: phylogenetic web repeater―an integrated and user-optimized framework for biomolecular phylogenetic analysis
phyml online―a web server for fast maximum likelihood-based phylogenetic inference
projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies
featureextract―extraction of sequence annotation made easy
dnamate: a consensus melting temperature prediction server for short dna sequences
stitchprofiles.uio.no: analysis of partly melted dna conformations using stitch profiles
dinamelt web server for nucleic acid melting prediction
dscheck: highly sensitive off-target search software for double-stranded rna-mediated rna interference
e-rnai: a web application to design optimized rnai constructs
t-profiler: scoring the activity of predefined groups of genes using gene expression data
gems: a web server for biclustering analysis of expression data
rnaloss: a web server for rna locally optimal secondary structures
kinefold web server for rna/dna folding path and structure prediction including pseudoknots and knots
oligowiz 2.0―integrating sequence feature annotation into the design of microarray probes
gepas, an experiment-oriented pipeline for the analysis of microarray gene expression data
arrayxpath ii: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using scalable vector ..
vampire microarray suite: a web-based platform for the interpretation of gene expression data
pathwayexplorer: web service for visualizing high-throughput expression data on biological pathways
race: remote analysis computation for gene expression data
midaw: a web tool for statistical analysis of microarray data
the foldalign web server for pairwise structural rna alignment and mutual motif search
t-stag: resource and web-interface for tissue-specific transcripts and genes
asian: a web server for inferring a regulatory network framework from gene expression profiles
targetidentifier: a webserver for identifying full-length cdnas from est sequences
gba server: est-based digital gene expression profiling
antihunter 2.0: increased speed and sensitivity in searching blast output for est antisense transcripts
orfpredictor: predicting protein-coding regions in est-derived sequences
asepcr: alternative splicing electronic rt
the trnascan-se, snoscan and snogps web servers for the detection of trnas and snornas
ribex: a web server for locating riboswitches and other conserved bacterial regulatory elements
websage: a web tool for visual analysis of differentially expressed human sage tags
microinspector: a web tool for detection of mirna binding sites in an rna sequence
miru: an automated plant mirna target prediction server
aismig―an interactive server-side molecule image generator
brigep―the bridge-based genome
gfinder: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists
the multilocus sequence typing network: mlst.net
the bioinformatics resource for oral pathogens
webgestalt: an integrated system for exploring gene sets in various biological contexts
genepath: from mutations to genetic networks and back
data mining tools for the saccharomyces cerevisiae morphological database
geneseeker: extraction and integration of human disease-related information from web-based genetic databases
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 dynamic biological databases
éclair―a web service for unravelling species origin of sequences sampled from mixed host interfaces
pubfinder: a tool for improving retrieval rate of relevant pubmed abstracts
litminer and wikigene: identifying problem-related key players of gene regulation using publication abstracts
gopubmed: exploring pubmed with the gene ontology
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