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

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W460-4.

PMID: 15215430 [PubMed - indexed for MEDLINE]
6246: Hokamp K, Roche FM, Acab M, Rousseau ME, Kuo B, Goode D, Aeschliman D,

Bryan J, Babiuk LA, Hancock RE, Brinkman FS.

ArrayPipe: a flexible processing pipeline for microarray data.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W457-9.

PMID: 15215429 [PubMed - indexed for MEDLINE]
6247: Khatri P, Bhavsar P, Bawa G, Draghici S.

Onto-Tools: an ensemble of web-accessible, ontology-based tools for the

functional design and interpretation of high-throughput gene expression

experiments.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W449-56.

PMID: 15215428 [PubMed - indexed for MEDLINE]

ArrayProspector: a web resource of functional associations inferred from

microarray expression data.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W445-8.

PMID: 15215427 [PubMed - indexed for MEDLINE]
6249: Cheung KH, Hager J, Pan D, Srivastava R, Mane S, Li Y, Miller P, Williams

KR.

microarray platforms.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W441-4.

PMID: 15215426 [PubMed - indexed for MEDLINE]

IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell

receptor V-J and V-D-J rearrangement analysis.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W435-40.

PMID: 15215425 [PubMed - indexed for MEDLINE]
6251: Muller C, Denis M, Gentzbittel L, Faraut T.

The Iccare web server: an attempt to merge sequence and mapping information for

plant and animal species.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W429-34.

PMID: 15215424 [PubMed - indexed for MEDLINE]
6252: Kalinina OV, Novichkov PS, Mironov AA, Gelfand MS, Rakhmaninova AB.

SDPpred: a tool for prediction of amino acid residues that determine

differences in functional specificity of homologous proteins.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W424-8.

PMID: 15215423 [PubMed - indexed for MEDLINE]
6253: Fu Y, Frith MC, Haverty PM, Weng Z.

MotifViz: an analysis and visualization tool for motif discovery.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W420-3.

PMID: 15215422 [PubMed - indexed for MEDLINE]

ESLpred: SVM-based method for subcellular localization of eukaryotic proteins

using dipeptide composition and PSI-BLAST.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W414-9.

PMID: 15215421 [PubMed - indexed for MEDLINE]
6255: Ansari MZ, Yadav G, Gokhale RS, Mohanty D.

NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W405-13.

PMID: 15215420 [PubMed - indexed for MEDLINE]

PRED-TMBB: a web server for predicting the topology of beta-barrel outer

membrane proteins.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W400-4.

PMID: 15215419 [PubMed - indexed for MEDLINE]
6257: Berven FS, Flikka K, Jensen HB, Eidhammer I.

BOMP: a program to predict integral beta-barrel outer membrane proteins encoded

within genomes of Gram-negative bacteria.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W394-9.

PMID: 15215418 [PubMed - indexed for MEDLINE]
6258: Arai M, Mitsuke H, Ikeda M, Xia JX, Kikuchi T, Satake M, Shimizu T.

ConPred II: a consensus prediction method for obtaining transmembrane topology

models with high reliability.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W390-3.

PMID: 15215417 [PubMed - indexed for MEDLINE]
6259: Bhasin M, Raghava GP.

GPCRpred: an SVM-based method for prediction of families and subfamilies of

G-protein coupled receptors.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W383-9.

PMID: 15215416 [PubMed - indexed for MEDLINE]
6260: Papasaikas PK, Bagos PG, Litou ZI, Promponas VJ, Hamodrakas SJ.

PRED-GPCR: GPCR recognition and family classification server.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W380-2.

PMID: 15215415 [PubMed - indexed for MEDLINE]

PrediSi: prediction of signal peptides and their cleavage positions.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W375-9.

PMID: 15215414 [PubMed - indexed for MEDLINE]

MITOPRED: a web server for the prediction of mitochondrial proteins.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W372-4.

PMID: 15215413 [PubMed - indexed for MEDLINE]

J, Macdonell C, Fyshe A, Meeuwis D.

Proteome Analyst: custom predictions with explanations in a web-based tool for

high-throughput proteome annotations.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W365-71.

PMID: 15215412 [PubMed - indexed for MEDLINE]

GDAP: a web tool for genome-wide protein disulfide bond prediction.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W360-4.

PMID: 15215411 [PubMed - indexed for MEDLINE]

SDPMOD: an automated comparative modeling server for small disulfide-bonded

proteins.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W356-9.

PMID: 15215410 [PubMed - indexed for MEDLINE]
6266: Lenffer J, Lai P, El Mejaber W, Khan AM, Koh JL, Tan PT, Seah SH, Brusic

V.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W350-5.

PMID: 15215409 [PubMed - indexed for MEDLINE]
6267: Levitsky VG.

RECON: a program for prediction of nucleosome formation potential.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W346-9.

PMID: 15215408 [PubMed - indexed for MEDLINE]

JS, Kelleher NL.

ProSight PTM: an integrated environment for protein identification and

characterization by top-down mass spectrometry.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W340-5.

PMID: 15215407 [PubMed - indexed for MEDLINE]

Phydbac2: improved inference of gene function using interactive phylogenomic

profiling and chromosomal location analysis.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W336-9.

PMID: 15215406 [PubMed - indexed for MEDLINE]
6270: Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Falquet L.

MyHits: a new interactive resource for protein annotation and domain

identification.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W332-5.

PMID: 15215405 [PubMed - indexed for MEDLINE]
6271: Marchler-Bauer A, Bryant SH.

CD-Search: protein domain annotations on the fly.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31.

PMID: 15215404 [PubMed - indexed for MEDLINE]

The PredictProtein server.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W321-6.

PMID: 15215403 [PubMed - indexed for MEDLINE]

PredictRegulon: a web server for the prediction of the regulatory protein

binding sites and operons in prokaryote genomes.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W318-20.

PMID: 15215402 [PubMed - indexed for MEDLINE]
6274: Groth D, Lehrach H, Hennig S.

GOblet: a platform for Gene Ontology annotation of anonymous sequence data.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W313-7.

PMID: 15215401 [PubMed - indexed for MEDLINE]

AUGUSTUS: a web server for gene finding in eukaryotes.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12.

PMID: 15215400 [PubMed - indexed for MEDLINE]

AGenDA: gene prediction by cross-species sequence comparison.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W305-8.

PMID: 15215399 [PubMed - indexed for MEDLINE]

e2g: an interactive web-based server for efficiently mapping large EST and cDNA

sets to genomic sequences.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W301-4.

PMID: 15215398 [PubMed - indexed for MEDLINE]
6278: Masseroli M, Martucci D, Pinciroli F.

GFINDer: Genome Function INtegrated Discoverer through dynamic annotation,

statistical analysis, and mining.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W293-300.

PMID: 15215397 [PubMed - indexed for MEDLINE]
6279: Oliver JL, Carpena P, Hackenberg M, Bernaola-Galvan P.

IsoFinder: computational prediction of isochores in genome sequences.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W287-92.

PMID: 15215396 [PubMed - indexed for MEDLINE]

ECR Browser: a tool for visualizing and accessing data from comparisons of

multiple vertebrate genomes.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W280-6.

PMID: 15215395 [PubMed - indexed for MEDLINE]
6281: Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I.

VISTA: computational tools for comparative genomics.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9.

PMID: 15215394 [PubMed - indexed for MEDLINE]

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures

of carbohydrate sugar chains.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W267-72.

PMID: 15215393 [PubMed - indexed for MEDLINE]
6283: Lohmann KK, von der Lieth CW.

GlycoFragment and GlycoSearchMS: web tools to support the interpretation of

mass spectra of complex carbohydrates.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W261-6.

PMID: 15215392 [PubMed - indexed for MEDLINE]
6284: Vega VB, Bangarusamy DK, Miller LD, Liu ET, Lin CY.

BEARR: Batch Extraction and Analysis of cis-Regulatory Regions.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W257-60.

PMID: 15215391 [PubMed - indexed for MEDLINE]

CREME: Cis-Regulatory Module Explorer for the human genome.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W253-6.

PMID: 15215390 [PubMed - indexed for MEDLINE]

ConSite: web-based prediction of regulatory elements using cross-species

comparison.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W249-52.

PMID: 15215389 [PubMed - indexed for MEDLINE]
6287: Conde L, Vaquerizas JM, Santoyo J, Al-Shahrour F, Ruiz-Llorente S,

Robledo M, Dopazo J.

PupaSNP Finder: a web tool for finding SNPs with putative effect at

transcriptional level.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W242-8.

PMID: 15215388 [PubMed - indexed for MEDLINE]

SeqVISTA: a new module of integrated computational tools for studying

transcriptional regulation.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W235-41.

PMID: 15215387 [PubMed - indexed for MEDLINE]
6289: Pan H, Zuo L, Choudhary V, Zhang Z, Leow SH, Chong FT, Huang Y, Ong VW,

Mohanty B, Tan SL, Krishnan SP, Bajic VB.

Dragon TF Association Miner: a system for exploring transcription factor

associations through text-mining.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W230-4.

PMID: 15215386 [PubMed - indexed for MEDLINE]

POBO, transcription factor binding site verification with bootstrapping.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W222-9.

PMID: 15215385 [PubMed - indexed for MEDLINE]

rVISTA 2.0: evolutionary analysis of transcription factor binding sites.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W217-21.

PMID: 15215384 [PubMed - indexed for MEDLINE]

CARRIE web service: automated transcriptional regulatory network inference and

interactive analysis.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W213-6.

PMID: 15215383 [PubMed - indexed for MEDLINE]
6293: Oshchepkov DY, Vityaev EE, Grigorovich DA, Ignatieva EV, Khlebodarova TM.
SITECON: a tool for detecting conservative conformational and physicochemical

properties in transcription factor binding site alignments and for site

recognition.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W208-12.

PMID: 15215382 [PubMed - indexed for MEDLINE]
6294: Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS.

A suite of web-based programs to search for transcriptional regulatory motifs.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W204-7.

PMID: 15215381 [PubMed - indexed for MEDLINE]

Weeder Web: discovery of transcription factor binding sites in a set of

sequences from co-regulated genes.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W199-203.

PMID: 15215380 [PubMed - indexed for MEDLINE]
6296: Alkema WB, Johansson O, Lagergren J, Wasserman WW.

MSCAN: identification of functional clusters of transcription factor binding

sites.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W195-8.

PromoSer: improvements to the algorithm, visualization and accessibility.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W191-4.

PMID: 15215378 [PubMed - indexed for MEDLINE]

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W187-90.

PMID: 15215377 [PubMed - indexed for MEDLINE]
6299: Kim N, Shin S, Lee S.

ASmodeler: gene modeling of alternative splicing from genomic alignment of

mRNA, EST and protein sequences.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W181-6.

PMID: 15215376 [PubMed - indexed for MEDLINE]
6300: Rouillard JM, Lee W, Truan G, Gao X, Zhou X, Gulari E.

Gene2Oligo: oligonucleotide design for in vitro gene synthesis.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W176-80.

PMID: 15215375 [PubMed - indexed for MEDLINE]

The sequencing-based typing tool of dbMHC: typing highly polymorphic gene

sequences.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W173-5.

PMID: 15215374 [PubMed - indexed for MEDLINE]
6302: Weckx S, De Rijk P, Van Broeckhoven C, Del-Favero J.

SNPbox: web-based high-throughput primer design from gene to genome.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W170-2.

PMID: 15215373 [PubMed - indexed for MEDLINE]

PDA: a pipeline to explore and estimate polymorphism in large DNA databases.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W166-9.

PMID: 15215372 [PubMed - indexed for MEDLINE]

H, Delfour O, Michot B, Gautheret D.

The ERPIN server: an interface to profile-based RNA motif identification.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W160-5.

PMID: 15215371 [PubMed - indexed for MEDLINE]
6305: Bengert P, Dandekar T.

Riboswitch finder--a tool for identification of riboswitch RNAs.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W154-9.

PMID: 15215370 [PubMed - indexed for MEDLINE]

RDfolder: a web server for prediction of RNA secondary structure.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W150-3.

PMID: 15215369 [PubMed - indexed for MEDLINE]

ILM: a web server for predicting RNA secondary structures with pseudoknots.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W146-9.

PMID: 15215368 [PubMed - indexed for MEDLINE]

CARNAC: folding families of related RNAs.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W142-5.

PMID: 15215367 [PubMed - indexed for MEDLINE]

Sfold web server for statistical folding and rational design of nucleic acids.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W135-41.

PMID: 15215366 [PubMed - indexed for MEDLINE]

siRNA Selection Server: an automated siRNA oligonucleotide prediction server.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W130-4.

PMID: 15215365 [PubMed - indexed for MEDLINE]

siDirect: highly effective, target-specific siRNA design software for mammalian

RNA interference.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W124-9.

PMID: 15215364 [PubMed - indexed for MEDLINE]
6312: Dudek P, Picard D.

TROD: T7 RNAi Oligo Designer.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W121-3.

PMID: 15215363 [PubMed - indexed for MEDLINE]

DEQOR: a web-based tool for the design and quality control of siRNAs.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W113-20.

PMID: 15215362 [PubMed - indexed for MEDLINE]

A web server for performing electronic PCR.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W108-12.

PMID: 15215361 [PubMed - indexed for MEDLINE]

Qgrid: clustering tool for detecting charged and hydrophobic regions in

proteins.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W104-7.

PMID: 15215360 [PubMed - indexed for MEDLINE]
6316: Guda C, Lu S, Scheeff ED, Bourne PE, Shindyalov IN.

CE-MC: a multiple protein structure alignment server.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W100-3.

PMID: 15215359 [PubMed - indexed for MEDLINE]

ClusPro: a fully automated algorithm for protein-protein docking.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W96-9.

PMID: 15215358 [PubMed - indexed for MEDLINE]

WebInterViewer: visualizing and analyzing molecular interaction networks.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W89-95.

PMID: 15215357 [PubMed - indexed for MEDLINE]

PathBLAST: a tool for alignment of protein interaction networks.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W83-8.

PMID: 15215356 [PubMed - indexed for MEDLINE]

ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary

substructures.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W76-82.

PMID: 15215355 [PubMed - indexed for MEDLINE]
6321: Zhang Z, Ng SK.

InterWeaver: interaction reports for discovering potential protein interaction

partners with online evidence.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W73-5.

PMID: 15215354 [PubMed - indexed for MEDLINE]
6322: Tan SH, Zhang Z, Ng SK.

ADVICE: Automated Detection and Validation of Interaction by Co-Evolution.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W69-72.

PMID: 15215353 [PubMed - indexed for MEDLINE]

CRASP: a program for analysis of coordinated substitutions in multiple

alignments of protein sequences.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W64-8.

PMID: 15215352 [PubMed - indexed for MEDLINE]
6324: Ray WC.

MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence

alignments.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W59-63.

PMID: 15215351 [PubMed - indexed for MEDLINE]
6325: Ohtsuka M, Horiuchi S, Kulski JK, Kimura M, Inoko H.

CHOP: visualization of 'wobbling' and isolation of highly conserved regions

from aligned DNA sequences.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W55-8.

PMID: 15215350 [PubMed - indexed for MEDLINE]
6326: Prasad JC, Vajda S, Camacho CJ.

Consensus alignment server for reliable comparative modeling with distant

templates.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W50-4.

PMID: 15215349 [PubMed - indexed for MEDLINE]
6327: Zika R, Paces J, Pavlicek A, Paces V.

WAViS server for handling, visualization and presentation of multiple

alignments of nucleotide or amino acids sequences.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W48-9.

PMID: 15215348 [PubMed - indexed for MEDLINE]
6328: Qi J, Luo H, Hao B.

CVTree: a phylogenetic tree reconstruction tool based on whole genomes.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W45-7.

PMID: 15215347 [PubMed - indexed for MEDLINE]

The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W41-4.

PMID: 15215346 [PubMed - indexed for MEDLINE]

3DCoffee@igs: a web server for combining sequences and structures into a

multiple sequence alignment.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40.

PMID: 15215345 [PubMed - indexed for MEDLINE]
6331: Morgenstern B.

DIALIGN: multiple DNA and protein sequence alignment at BiBiServ.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W33-6.

PMID: 15215344 [PubMed - indexed for MEDLINE]

BLAST Filter and GraphAlign: rule-based formation and analysis of sets of

related DNA and protein sequences.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W26-32.

PMID: 15215343 [PubMed - indexed for MEDLINE]
6333: McGinnis S, Madden TL.

BLAST: at the core of a powerful and diverse set of sequence analysis tools.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W20-5.