1: Im eo, Chee W, Lim hj, Bender M, Tsai hm, Yang so, Lee H

[Treatment strategy for children with Wilms tumor]

Nippon Geka Gakkai Zasshi. 2005 Jul;106(7):422-6. Review. Japanese.

PMID: 16045185 [PubMed - indexed for MEDLINE]

PRISM: protein interactions by structural matching.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W331-6.

PMID: 15991339 [PubMed - indexed for MEDLINE]

SVC: structured visualization of evolutionary sequence conservation.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W271-3.

PMID: 15991338 [PubMed - indexed for MEDLINE]

MEDock: a web server for efficient prediction of ligand binding sites based on

a novel optimization algorithm.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W233-8.

PMID: 15991337 [PubMed - indexed for MEDLINE]
2914: Bhasin M, Raghava GP.

Pcleavage: an SVM based method for prediction of constitutive proteasome and

immunoproteasome cleavage sites in antigenic sequences.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W202-7.

PMID: 15988831 [PubMed - indexed for MEDLINE]
2915: Kumar M, Bhasin M, Natt NK, Raghava GP.

BhairPred: prediction of beta-hairpins in a protein from multiple alignment

information using ANN and SVM techniques.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W154-9.

PMID: 15988830 [PubMed - indexed for MEDLINE]
2916: Ivanisenko VA, Eroshkin AM, Kolchanov NA.

WebProAnalyst: an interactive tool for analysis of quantitative

structure-activity relationships in protein families.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W99-104.

PMID: 15980590 [PubMed - indexed for MEDLINE]
2917: Wang G, Dunbrack RL Jr.

PISCES: recent improvements to a PDB sequence culling server.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W94-8.

PMID: 15980589 [PubMed - indexed for MEDLINE]

ProFunc: a server for predicting protein function from 3D structure.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W89-93.

PMID: 15980588 [PubMed - indexed for MEDLINE]

Fragment Finder: a web-based software to identify similar three-dimensional

structural motif.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W85-8.

PMID: 15980587 [PubMed - indexed for MEDLINE]
2920: Sasson O, Linial M.

ProTarget: automatic prediction of protein structure novelty.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W81-4.

PMID: 15980586 [PubMed - indexed for MEDLINE]

GoPubMed: exploring PubMed with the Gene Ontology.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W783-6.

PMID: 15980585 [PubMed - indexed for MEDLINE]

Schneider R.

LitMiner and WikiGene: identifying problem-related key players of gene

regulation using publication abstracts.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W779-82.

PMID: 15980584 [PubMed - indexed for MEDLINE]

PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W774-8.

PMID: 15980583 [PubMed - indexed for MEDLINE]

Current Comparative Table (CCT) automates customized searches of dynamic

biological databases.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W770-3.

PMID: 15980582 [PubMed - indexed for MEDLINE]
2925: Hung LH, Ngan SC, Liu T, Samudrala R.

PROTINFO: new algorithms for enhanced protein structure predictions.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W77-80.

PMID: 15980581 [PubMed - indexed for MEDLINE]

MRS: a fast and compact retrieval system for biological data.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W766-9.

PMID: 15980580 [PubMed - indexed for MEDLINE]

Recent additions and improvements to the Onto-Tools.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W762-5.

PMID: 15980579 [PubMed - indexed for MEDLINE]

G.

from web-based genetic databases.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W758-61.

PMID: 15980578 [PubMed - indexed for MEDLINE]

Data mining tools for the Saccharomyces cerevisiae morphological database.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W753-7.

PMID: 15980577 [PubMed - indexed for MEDLINE]

GenePath: from mutations to genetic networks and back.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W749-52.

PMID: 15980576 [PubMed - indexed for MEDLINE]

WebGestalt: an integrated system for exploring gene sets in various biological

contexts.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W741-8.

PMID: 15980575 [PubMed - indexed for MEDLINE]
2932: Chen T, Abbey K, Deng WJ, Cheng MC.

The bioinformatics resource for oral pathogens.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W734-40.

PMID: 15980574 [PubMed - indexed for MEDLINE]

The multilocus sequence typing network: mlst.net.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W728-33.

PMID: 15980573 [PubMed - indexed for MEDLINE]

Eclair--a web service for unravelling species origin of sequences sampled from

mixed host interfaces.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W724-7.

PMID: 15980572 [PubMed - indexed for MEDLINE]
2935: Cheng J, Randall AZ, Sweredoski MJ, Baldi P.

SCRATCH: a protein structure and structural feature prediction server.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W72-6.

PMID: 15980571 [PubMed - indexed for MEDLINE]

GFINDer: genetic disease and phenotype location statistical analysis and mining

of dynamically annotated gene lists.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W717-23.

PMID: 15980570 [PubMed - indexed for MEDLINE]
2937: Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S,

Paczian T, Wilke A, Meyer F.

BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W710-6.

PMID: 15980569 [PubMed - indexed for MEDLINE]
2938: Bohne-Lang A, Groch WD, Ranzinger R.

AISMIG--an interactive server-side molecule image generator.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W705-9.

PMID: 15980568 [PubMed - indexed for MEDLINE]

miRU: an automated plant miRNA target prediction server.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W701-4.

PMID: 15980567 [PubMed - indexed for MEDLINE]

MicroInspector: a web tool for detection of miRNA binding sites in an RNA

sequence.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W696-700.

PMID: 15980566 [PubMed - indexed for MEDLINE]
2941: Pylouster J, Senamaud-Beaufort C, Saison-Behmoaras TE.

WEBSAGE: a web tool for visual analysis of differentially expressed human SAGE

tags.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W693-5.

RibEx: a web server for locating riboswitches and other conserved bacterial

regulatory elements.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W690-2.

PMID: 15980564 [PubMed - indexed for MEDLINE]
2943: Schattner P, Brooks AN, Lowe TM.

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and

snoRNAs.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W686-9.

PMID: 15980563 [PubMed - indexed for MEDLINE]
2944: Kim N, Lim D, Lee S, Kim H.

ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W681-5.

PMID: 15980562 [PubMed - indexed for MEDLINE]

OrfPredictor: predicting protein-coding regions in EST-derived sequences.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W677-80.

PMID: 15980561 [PubMed - indexed for MEDLINE]

GBA server: EST-based digital gene expression profiling.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W673-6.

PMID: 15980560 [PubMed - indexed for MEDLINE]

TargetIdentifier: a webserver for identifying full-length cDNAs from EST

sequences.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W669-72.

PMID: 15980559 [PubMed - indexed for MEDLINE]
2948: Lavorgna G, Triunfo R, Santoni F, Orfanelli U, Noci S, Bulfone A, Zanetti

G, Casari G.

AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for

EST antisense transcripts.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W665-8.

PMID: 15980558 [PubMed - indexed for MEDLINE]

ASIAN: a web server for inferring a regulatory network framework from gene

expression profiles.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W659-64.

PMID: 15980557 [PubMed - indexed for MEDLINE]
2950: Gupta S, Vingron M, Haas SA.

T-STAG: resource and web-interface for tissue-specific transcripts and genes.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W654-8.

PMID: 15980556 [PubMed - indexed for MEDLINE]

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif

search.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W650-3.

PAT: a protein analysis toolkit for integrated biocomputing on the web.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W65-71.

PMID: 15980554 [PubMed - indexed for MEDLINE]

MIDAW: a web tool for statistical analysis of microarray data.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W644-9.

PMID: 15980553 [PubMed - indexed for MEDLINE]

RACE: Remote Analysis Computation for gene Expression data.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W638-43.

PMID: 15980552 [PubMed - indexed for MEDLINE]

Z.

biological pathways.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W633-7.

PMID: 15980551 [PubMed - indexed for MEDLINE]

VAMPIRE microarray suite: a web-based platform for the interpretation of gene

expression data.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W627-32.

PMID: 15980550 [PubMed - indexed for MEDLINE]
2957: Chung HJ, Park CH, Han MR, Lee S, Ohn JH, Kim J, Kim J, Kim JH.

ArrayXPath II: mapping and visualizing microarray gene-expression data with

biomedical ontologies and integrated biological pathway resources using Scalable

Vector Graphics.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W621-6.

PMID: 15980549 [PubMed - indexed for MEDLINE]

R, Al-Shahrour F, Herrero J, Dopazo J.

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene

expression data.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W616-20.

PMID: 15980548 [PubMed - indexed for MEDLINE]

OligoWiz 2.0--integrating sequence feature annotation into the design of

microarray probes.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W611-5.

PMID: 15980547 [PubMed - indexed for MEDLINE]
2960: Xayaphoummine A, Bucher T, Isambert H.

Kinefold web server for RNA/DNA folding path and structure prediction including

pseudoknots and knots.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W605-10.

PMID: 15980546 [PubMed - indexed for MEDLINE]
2961: Clote P.

RNALOSS: a web server for RNA locally optimal secondary structures.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W600-4.

PMID: 15980545 [PubMed - indexed for MEDLINE]

GEMS: a web server for biclustering analysis of expression data.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W596-9.

PMID: 15980544 [PubMed - indexed for MEDLINE]

T-profiler: scoring the activity of predefined groups of genes using gene

expression data.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W592-5.

PMID: 15980543 [PubMed - indexed for MEDLINE]
2964: Naito Y, Yamada T, Matsumiya T, Ui-Tei K, Saigo K, Morishita S.

dsCheck: highly sensitive off-target search software for double-stranded

RNA-mediated RNA interference.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W589-91.

PMID: 15980542 [PubMed - indexed for MEDLINE]
2965: Arziman Z, Horn T, Boutros M.

E-RNAi: a web application to design optimized RNAi constructs.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W582-8.

PMID: 15980541 [PubMed - indexed for MEDLINE]

DINAMelt web server for nucleic acid melting prediction.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W577-81.

PMID: 15980540 [PubMed - indexed for MEDLINE]

Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch

profiles.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W573-6.

PMID: 15980539 [PubMed - indexed for MEDLINE]
2968: Panjkovich A, Norambuena T, Melo F.

dnaMATE: a consensus melting temperature prediction server for short DNA

sequences.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W570-2.

PMID: 15980538 [PubMed - indexed for MEDLINE]
2969: Wernersson R.

FeatureExtract--extraction of sequence annotation made easy.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W567-9.

PMID: 15980537 [PubMed - indexed for MEDLINE]

Projector 2: contig mapping for efficient gap-closure of prokaryotic genome

sequence assemblies.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W560-6.

PMID: 15980536 [PubMed - indexed for MEDLINE]
2971: Loots GG, Ovcharenko I.

Dcode.org anthology of comparative genomic tools.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W56-64.

PMID: 15980535 [PubMed - indexed for MEDLINE]

PHYML Online--a web server for fast maximum likelihood-based phylogenetic

inference.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W557-9.

PMID: 15980534 [PubMed - indexed for MEDLINE]
2973: Lin CY, Lin FK, Lin CH, Lai LW, Hsu HJ, Chen SH, Hsiung CA.

POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework

for biomolecular phylogenetic analysis.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W553-6.

PMID: 15980533 [PubMed - indexed for MEDLINE]
2974: Ringquist S, Pecoraro C, Gilchrist CM, Styche A, Rudert WA, Benos PV,

Trucco M.

SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of

human and mouse polymorphisms.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W548-52.

PMID: 15980532 [PubMed - indexed for MEDLINE]

MuPlex: multi-objective multiplex PCR assay design.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W544-7.

PMID: 15980531 [PubMed - indexed for MEDLINE]

YASS: enhancing the sensitivity of DNA similarity search.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W540-3.

PMID: 15980530 [PubMed - indexed for MEDLINE]

PARALIGN: rapid and sensitive sequence similarity searches powered by parallel

computing technology.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W535-9.

PMID: 15980529 [PubMed - indexed for MEDLINE]
2978: Pohler D, Werner N, Steinkamp R, Morgenstern B.

Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W532-4.

PMID: 15980528 [PubMed - indexed for MEDLINE]

JCat: a novel tool to adapt codon usage of a target gene to its potential

expression host.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W526-31.

PMID: 15980527 [PubMed - indexed for MEDLINE]
2980: Rydzanicz R, Zhao XS, Johnson PE.

Assembly PCR oligo maker: a tool for designing oligodeoxynucleotides for

constructing long DNA molecules for RNA production.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W521-5.

PMID: 15980526 [PubMed - indexed for MEDLINE]
2981: Fredslund J, Schauser L, Madsen LH, Sandal N, Stougaard J.

PriFi: using a multiple alignment of related sequences to find primers for

amplification of homologs.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W516-20.

PMID: 15980525 [PubMed - indexed for MEDLINE]
2982: Fertil B, Massin M, Lespinats S, Devic C, Dumee P, Giron A.

GENSTYLE: exploration and analysis of DNA sequences with genomic signature.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W512-5.

PMID: 15980524 [PubMed - indexed for MEDLINE]

AMOD: a morpholino oligonucleotide selection tool.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W506-11.

PMID: 15980523 [PubMed - indexed for MEDLINE]

pathological effect in genes, for genotyping purposes.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W501-5.

PMID: 15980522 [PubMed - indexed for MEDLINE]

CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural

biology.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W50-5.

PMID: 15980521 [PubMed - indexed for MEDLINE]
2986: Klaften M, Hrabe de Angelis M.

ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping

panels for the SNP genotyping of mouse mutants.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W496-500.

PMID: 15980520 [PubMed - indexed for MEDLINE]
2987: Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GA, Mongin E, Barker

G, Spangenberg GC, Edwards D.

SNPServer: a real-time SNP discovery tool.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W493-5.

PMID: 15980519 [PubMed - indexed for MEDLINE]
2988: Zhang R, Zhu Z, Zhu H, Nguyen T, Yao F, Xia K, Liang D, Liu C.

SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W489-92.

PMID: 15980518 [PubMed - indexed for MEDLINE]

SNPAnalyzer: a web-based integrated workbench for single-nucleotide

polymorphism analysis.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W483-8.

PMID: 15980517 [PubMed - indexed for MEDLINE]
2990: Bao L, Zhou M, Cui Y.

nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide

polymorphisms.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W480-2.

PMID: 15980516 [PubMed - indexed for MEDLINE]
2991: Cruveiller S, Le Saux J, Vallenet D, Lajus A, Bocs S, Medigue C.

MICheck: a web tool for fast checking of syntactic annotations of bacterial

genomes.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W471-9.

PMID: 15980515 [PubMed - indexed for MEDLINE]
2992: Olason PI.

Integrating protein annotation resources through the Distributed Annotation

System.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W468-70.

AUGUSTUS: a web server for gene prediction in eukaryotes that allows

user-defined constraints.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W465-7.

PMID: 15980513 [PubMed - indexed for MEDLINE]
2994: Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J.

BABELOMICS: a suite of web tools for functional annotation and analysis of

groups of genes in high-throughput experiments.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W460-4.

PMID: 15980512 [PubMed - indexed for MEDLINE]
2995: Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu

P, Szafron D, Greiner R, Wishart DS.

BASys: a web server for automated bacterial genome annotation.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W455-9.

PMID: 15980511 [PubMed - indexed for MEDLINE]
2996: Besemer J, Borodovsky M.

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4.

PMID: 15980510 [PubMed - indexed for MEDLINE]

CONREAL web server: identification and visualization of conserved transcription

factor binding sites.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W447-50.

PMID: 15980509 [PubMed - indexed for MEDLINE]
2998: Corcoran DL, Feingold E, Benos PV.

FOOTER: a web tool for finding mammalian DNA regulatory regions using

phylogenetic footprinting.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W442-6.

PMID: 15980508 [PubMed - indexed for MEDLINE]
2999: Alland C, Moreews F, Boens D, Carpentier M, Chiusa S, Lonquety M, Renault