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《核酸研究医学期刊》2007年第14期

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conducting research on the web: 00 update for the bioinformatics links directory
web services at the european bioinformatics institute
etblast: a web server to identify expert reviewers appropriate journals and similar publications
cargo: a web portal to integrate customized biological information
ihop web services
berkeley phylogenomics group web servers: resources for structural phylogenomic analysis
multiphyl: a high-throughput phylogenomics webserver using distributed computing
phylemon: a suite of web tools for molecular evolution phylogenetics and phylogenomics
oligocalc: an online oligonucleotide properties calculator
dymhc: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features
crisprfinder: a web tool to identify clustered regularly interspaced short palindromic repeats
repk: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis
primerz: streamlined primer design for promoters exons and human snps
ntmg (n-terminal truncated mutants generator for cdna): an automatic multiplex pcr assays design for generating various n-terminal truncated cdna mutants
primerplus an enhanced web interface to primer
asterias: integrated analysis of expression and acgh data using an open-source web-based parallelized software suite
isacgh: a web-based environment for the analysis of array cgh and gene expression which includes functional profiling
magma: analysis of two-channel microarrays made easy
fatigo +: a functional profiling tool for genomic data. integration of functional annotation regulatory motifs and interaction data with microarray experiments
mobilomefinder: web-based tools for in silico and experimental discovery of bacterial genomic islands
cross-species microarray analysis with the oscar system suggests an insr->pax->nqo neuro-protective pathway in aging and alzheimer
quicksnp: an automated web server for selection of tagsnps
fgf: a web tool for fishing gene family in a whole genome database
optimizer: a web server for optimizing the codon usage of dna sequences
codono: codon usage bias analysis within and across genomes
webtraceminer: a web service for processing and mining est sequence trace files
estexplorer: an expressed sequence tag (est) assembly and annotation platform
wheat estimated transcript server (whets): a tool to provide best estimate of hexaploid wheat transcript sequence
genehub-gepis: digital expression profiling for normal and cancer tissues based on an integrated gene database
estpass: a web-based server for processing and annotating expressed sequence tag (est) sequences
sagexplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation
david bioinformatics resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
pathexpress: a web-based tool to identify relevant pathways in gene expression data
kaas: an automatic genome annotation and pathway reconstruction server
genetrail
g:profiler
madap a flexible clustering tool for the interpretation of one-dimensional genome annotation data
onto-tools: new additions and improvements in 00
update of the gd tool for prioritization of gene candidates to inherited diseases
webmotifs: automated discovery filtering and scoring of dna sequence motifs using multiple programs and bayesian approaches
stamp: a web tool for exploring dna-binding motif similarities
mybs: a comprehensive web server for mining transcription factor binding sites in yeast
rtanalyzer: a web application for finding new retrotransposons and detecting l retrotransposition signatures
the gibbs centroid sampler
flugenome: a web tool for genotyping influenza a virus
flan: a web server for influenza virus genome annotation
opossum: integrated tools for analysis of regulatory motif over-representation
melina ii: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
pap: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis
scope: a web server for practical de novo motif discovery
ltr_finder: an efficient tool for the prediction of full-length ltr retrotransposons
spliceport
bipass: bioinformatics pipeline alternative splicing services
astalavista: dynamic and flexible analysis of alternative splicing events in custom gene datasets
radar: a web server for rna data analysis and research
rnabor: a web server for rna structural neighbors
info-rna
rsre: rna structural robustness evaluator
pknotsrg: rna pseudoknot folding including near-optimal structures and sliding windows
taverna: a web suite for rna algorithms and applications
rna movies : sequential animation of rna secondary structures
the rnaz web server: prediction of thermodynamically stable and evolutionarily conserved rna structures
mipred: classification of real and pseudo microrna precursors using random forest prediction model with combined features
tfam .0: an online trna function classifier
domac: an accurate hybrid protein domain prediction server
pipe: protein interface/interior prediction engine
mt: a comparative protein structure modeling server
pcons.net: protein structure prediction meta server
molprobity: all-atom contacts and structure validation for proteins and nucleic acids
structure snp (stsnp): a web server for mapping and modeling nssnps on protein structures with linkage to metabolic pathways
dbali tools: mining the protein structure space
-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
nq-flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
prosa-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
qscop-blast
dlogo: a web server for the identification analysis and use of conserved protein substructures
pknot: the protein knot web server
protein knot server: detection of knots in protein structures
signal peptide prediction
myhits: improvements to an interactive resource for analyzing protein sequences
fastscop: a fast web server for recognizing protein structural domains and scop superfamilies
protsweep dsweep and domainsweep: protein analysis suite at dkfz
sh-hunter: discovery of sh domain interaction sites in proteins
the slimdisc server: short linear motif discovery in proteins
prdos: prediction of disordered protein regions from amino acid sequence
ipda: integrated protein disorder analyzer
pic: protein interactions calculator
minactionpath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape
pmg: online generation of high-quality molecular pictures and storyboarded animations
sitefinder|d: a web-based tool for predicting the location of functional sites in proteins
sequence harmony: detecting functional specificity from alignments
fralanyzer: a tool for functional analysis of fold-recognition sequence
par-d: a server to predict protein active site residues
selecton 00: advanced models for detecting positive and purifying selection using a bayesian inference approach
a server and database for dipole moments of proteins
pdbpqr: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
patch finder plus (pfplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces
the rci server: rapid and accurate calculation of protein flexibility using chemical shifts
cytosvm: an advanced server for identification of cytokine-receptor interactions
promateus
modpropep: a program for knowledge-based modeling of protein
fastcontact: a free energy scoring tool for protein
d-partner: a web server to infer interacting partners and binding models
frog: a free online drug d conformation generator
firestar
binding sites in proteins
wolf psort: protein localization predictor
kinasephos .0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns
canpredict: a computational tool for predicting cancer-associated missense mutations
zinc finger targeter (zifit): an engineered zinc finger/target site design tool
lipid maps online tools for lipid research
metapath online: a web server implementation of the network expansion algorithm
deep
visant .0: new modules for pathway visualization editing prediction and construction
indelscan: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events
re-music: a tool for multiple sequence alignment with regular expression constraints
the m-coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods
promals web server for accurate multiple protein sequence alignments
compass server for remote homology inference
dial: a web server for the pairwise alignment of two rna three-dimensional structures using nucleotide dihedral angle and base-pairing similarities
multiple whole genome alignments and novel biomedical applications at the vista portal
eprobalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities
blasto: a tool for searching orthologous groups
sepacs
biobayesnet: a web server for feature extraction and bayesian network modeling of biological sequence data
evaller: a web server for in silico assessment of potential protein allergenicity
prosight ptm .0: improved protein identification and characterization for top down mass spectrometry
the multi-q web server for multiplexed protein quantitation
dshift: a web server for predicting dna chemical shifts
crysttwiv: a webserver for automated phase extension and refinement in x-ray crystallography
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