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Volume 39, Issue suppl_2, 1 July 2011
Web Server issue
Editorial
Editorial
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W1–W2, https://doi.org/10.1093/nar/gkr515
Articles
Nucleic Acids Research: VOLUME 39 WEB SERVER ISSUE JULY 1, 2011
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Page i, https://doi.org/10.1093/nar/gkr570
The 2011 bioinformatics links directory update: more resources, tools and databases and features to empower the bioinformatics community
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W3–W7, https://doi.org/10.1093/nar/gkr514
PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W8–W12, https://doi.org/10.1093/nar/gkr244
Nucleic Acids Research
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Page ii, https://doi.org/10.1093/nar/gkr569
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W13–W17, https://doi.org/10.1093/nar/gkr245
iPBA: a tool for protein structure comparison using sequence alignment strategies
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W18–W23, https://doi.org/10.1093/nar/gkr333
CLICK—topology-independent comparison of biomolecular 3D structures
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W24–W28, https://doi.org/10.1093/nar/gkr393
HMMER web server: interactive sequence similarity searching
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W29–W37, https://doi.org/10.1093/nar/gkr367
FFAS server: novel features and applications
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W38–W44, https://doi.org/10.1093/nar/gkr441
R3D-BLAST: a search tool for similar RNA 3D substructures
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W45–W49, https://doi.org/10.1093/nar/gkr379
WebFR3D—a server for finding, aligning and analyzing recurrent RNA 3D motifs
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W50–W55, https://doi.org/10.1093/nar/gkr249
SLiMSearch 2.0: biological context for short linear motifs in proteins
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W56–W60, https://doi.org/10.1093/nar/gkr402
PHUSER (Primer Help for USER): a novel tool for USER fusion primer design
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W61–W67, https://doi.org/10.1093/nar/gkr394
CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W68–W73, https://doi.org/10.1093/nar/gkr316
ConTra v2: a tool to identify transcription factor binding sites across species, update 2011
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W74–W78, https://doi.org/10.1093/nar/gkr355
Genome surveyor 2.0: cis- regulatory analysis in Drosophila
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W79–W85, https://doi.org/10.1093/nar/gkr291
RSAT 2011: regulatory sequence analysis tools
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W86–W91, https://doi.org/10.1093/nar/gkr377
The RNAmute web server for the mutational analysis of RNA secondary structures
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W92–W99, https://doi.org/10.1093/nar/gkr207
Subscriptions
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Page iii, https://doi.org/10.1093/nar/gkr571
CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W100–W106, https://doi.org/10.1093/nar/gkr290
The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W107–W111, https://doi.org/10.1093/nar/gkr248
DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W112–W117, https://doi.org/10.1093/nar/gkr357
ncFANs: a web server for functional annotation of long non-coding RNAs
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W118–W124, https://doi.org/10.1093/nar/gkr432
miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W125–W131, https://doi.org/10.1093/nar/gkr374
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W132–W138, https://doi.org/10.1093/nar/gkr247
mirAct: a web tool for evaluating microRNA activity based on gene expression data
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W139–W144, https://doi.org/10.1093/nar/gkr351
DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W145–W148, https://doi.org/10.1093/nar/gkr294
RNApredator: fast accessibility-based prediction of sRNA targets
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W149–W154, https://doi.org/10.1093/nar/gkr467
psRNATarget: a plant small RNA target analysis server
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W155–W159, https://doi.org/10.1093/nar/gkr319
corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W160–W166, https://doi.org/10.1093/nar/gkr358
MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W167–W170, https://doi.org/10.1093/nar/gkr490
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W171–W176, https://doi.org/10.1093/nar/gkr184
KINARI-Web: a server for protein rigidity analysis
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W177–W183, https://doi.org/10.1093/nar/gkr482
AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W184–W189, https://doi.org/10.1093/nar/gkr430
CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W190–W196, https://doi.org/10.1093/nar/gkr411
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W197–W202, https://doi.org/10.1093/nar/gkr292
SA-Mot: a web server for the identification of motifs of interest extracted from protein loops
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W203–W209, https://doi.org/10.1093/nar/gkr410
The FALC-Loop web server for protein loop modeling
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W210–W214, https://doi.org/10.1093/nar/gkr352
SDM—a server for predicting effects of mutations on protein stability and malfunction
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W215–W222, https://doi.org/10.1093/nar/gkr363
GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W223–W228, https://doi.org/10.1093/nar/gkr412
PRUNE and PROBE—two modular web services for protein–protein docking
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W229–W234, https://doi.org/10.1093/nar/gkr317
firestar —advances in the prediction of functionally important residues
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W235–W241, https://doi.org/10.1093/nar/gkr437
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W242–W248, https://doi.org/10.1093/nar/gkr356
Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W249–W253, https://doi.org/10.1093/nar/gkr431
PAComplex: a web server to infer peptide antigen families and binding models from TCR–pMHC complexes
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W254–W260, https://doi.org/10.1093/nar/gkr434
Swimming into peptidomimetic chemical space using pepMMsMIMIC
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W261–W269, https://doi.org/10.1093/nar/gkr287
SwissDock, a protein-small molecule docking web service based on EADock DSS
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W270–W277, https://doi.org/10.1093/nar/gkr366
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W278–W282, https://doi.org/10.1093/nar/gkr389
PredUs: a web server for predicting protein interfaces using structural neighbors
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W283–W287, https://doi.org/10.1093/nar/gkr311
MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W288–W292, https://doi.org/10.1093/nar/gkr365
RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W293–W301, https://doi.org/10.1093/nar/gkr507
ADGO 2.0: interpreting microarray data and list of genes using composite annotations
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W302–W306, https://doi.org/10.1093/nar/gkr392
g:Profiler—a web server for functional interpretation of gene lists (2011 update)
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W307–W315, https://doi.org/10.1093/nar/gkr378
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W316–W322, https://doi.org/10.1093/nar/gkr483
BioProfiling.de: analytical web portal for high-throughput cell biology
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W323–W327, https://doi.org/10.1093/nar/gkr372
AnnotQTL: a new tool to gather functional and comparative information on a genomic region
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W328–W333, https://doi.org/10.1093/nar/gkr361
PINTA: a web server for network-based gene prioritization from expression data
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W334–W338, https://doi.org/10.1093/nar/gkr289
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W339–W346, https://doi.org/10.1093/nar/gkr466
PHAST: A Fast Phage Search Tool
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W347–W352, https://doi.org/10.1093/nar/gkr485
GCView: the genomic context viewer for protein homology searches
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W353–W356, https://doi.org/10.1093/nar/gkr364
MarkUs: a server to navigate sequence–structure–function space
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W357–W361, https://doi.org/10.1093/nar/gkr468
NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W362–W367, https://doi.org/10.1093/nar/gkr323
PILGRM: an interactive data-driven discovery platform for expert biologists
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W368–W374, https://doi.org/10.1093/nar/gkr440
MemPype: a pipeline for the annotation of eukaryotic membrane proteins
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W375–W380, https://doi.org/10.1093/nar/gkr282
PepServe: a web server for peptide analysis, clustering and visualization
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W381–W384, https://doi.org/10.1093/nar/gkr318
Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W385–W390, https://doi.org/10.1093/nar/gkr284
CENTDIST: discovery of co-associated factors by motif distribution
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W391–W399, https://doi.org/10.1093/nar/gkr387
GLAMM: Genome-Linked Application for Metabolic Maps
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W400–W405, https://doi.org/10.1093/nar/gkr433
The University of Minnesota Pathway Prediction System: multi-level prediction and visualization
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W406–W411, https://doi.org/10.1093/nar/gkr200
iPath2.0: interactive pathway explorer
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W412–W415, https://doi.org/10.1093/nar/gkr313
mirConnX: condition-specific mRNA-microRNA network integrator
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W416–W423, https://doi.org/10.1093/nar/gkr276
ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W424–W429, https://doi.org/10.1093/nar/gkr359
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W430–W436, https://doi.org/10.1093/nar/gkr332
ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W437–W443, https://doi.org/10.1093/nar/gkr391
SNPsyn: detection and exploration of SNP–SNP interactions
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W444–W449, https://doi.org/10.1093/nar/gkr321
CoPub update: CoPub 5.0 a text mining system to answer biological questions
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W450–W454, https://doi.org/10.1093/nar/gkr310
Génie: literature-based gene prioritization at multi genomic scale
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W455–W461, https://doi.org/10.1093/nar/gkr246
BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W462–W469, https://doi.org/10.1093/nar/gkr285
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W470–W474, https://doi.org/10.1093/nar/gkr408
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W475–W478, https://doi.org/10.1093/nar/gkr201
PhyleasProg: a user-oriented web server for wide evolutionary analyses
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W479–W485, https://doi.org/10.1093/nar/gkr243
ChemMine tools: an online service for analyzing and clustering small molecules
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W486–W491, https://doi.org/10.1093/nar/gkr320
DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical–protein interactome
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W492–W498, https://doi.org/10.1093/nar/gkr299
Detecting selection in immunoglobulin sequences
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W499–W504, https://doi.org/10.1093/nar/gkr413
ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W505–W510, https://doi.org/10.1093/nar/gkr403
R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W511–W517, https://doi.org/10.1093/nar/gkr288
CoMet—a web server for comparative functional profiling of metagenomes
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W518–W523, https://doi.org/10.1093/nar/gkr388
PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W524–W527, https://doi.org/10.1093/nar/gkr373
The BioExtract Server: a web-based bioinformatic workflow platform
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W528–W532, https://doi.org/10.1093/nar/gkr286
Web Services
Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W533–W540, https://doi.org/10.1093/nar/gkr353
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W541–W545, https://doi.org/10.1093/nar/gkr469
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W546–W550, https://doi.org/10.1093/nar/gkr438
Stand Alone Programs
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W551–W556, https://doi.org/10.1093/nar/gkr312
HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W557–W561, https://doi.org/10.1093/nar/gkr354
PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W562–W566, https://doi.org/10.1093/nar/gkr439
inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data
Nucleic Acids Research, Volume 39, Issue suppl_2, 1 July 2011, Pages W567–W575, https://doi.org/10.1093/nar/gkr506
