Works matching IS 03051048 AND DT 2007 AND VI 35 AND IP suppl_2

Results: 132

Editorial.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W1, doi. 10.1093/nar/gkm484

By:

Benson, Gary

Publication type:

Article

DEEP—A tool for differential expression effector prediction.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W619, doi. 10.1093/nar/gkm469

By:

Degenhardt, Jost;
Haubrock, Martin;
Dönitz, Jürgen;
Wingender, Edgar;
Crass, Torsten

Publication type:

Article

Conducting Research on the Web: 2007 Update for the Bioinformatics Links Directory.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W3, doi. 10.1093/nar/gkm459

By:

Fox, Joanne A.;
McMillan, Scott;
Ouellette, B. F. Francis

Publication type:

Article

SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W163, doi. 10.1093/nar/gkm429

By:

Norambuena, Tomás;
Malig, Rodrigo;
Melo, Francisco

Publication type:

Article

SplicePort—An interactive splice-site analysis tool.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W285, doi. 10.1093/nar/gkm407

By:

Dogan, Rezarta Islamaj;
Getoor, Lise;
Wilbur, W. John;
Mount, Stephen M.

Publication type:

Article

oPOSSUM: integrated tools for analysis of regulatory motif over-representation.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W245, doi. 10.1093/nar/gkm427

By:

Ho Sui, Shannan J.;
Fulton, Debra L.;
Arenillas, David J.;
Kwon, Andrew T.;
Wasserman, Wyeth W.

Publication type:

Article

PIC: Protein Interactions Calculator.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W473, doi. 10.1093/nar/gkm423

By:

Tina, K. G.;
Bhadra, R.;
Srinivasan, N.

Publication type:

Article

siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W489, doi. 10.1093/nar/gkm422

By:

Innis, C. Axel

Publication type:

Article

DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W169, doi. 10.1093/nar/gkm415

By:

Huang, Da Wei;
Sherman, Brad T.;
Tan, Qina;
Kir, Joseph;
Liu, David;
Bryant, David;
Guo, Yongjian;
Stephens, Robert;
Baseler, Michael W.;
Lane, H. Clifford;
Lempicki, Richard A.

Publication type:

Article

Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W105

By:

Lu, Yue;
He, Xin;
Zhong, Sheng

Publication type:

Article

FGF: A web tool for Fishing Gene Family in a whole genome database.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W121, doi. 10.1093/nar/gkm426

By:

Zheng, Hongkun;
Shi, Junjie;
Fang, Xiaodong;
Li, Yuan;
Vang, Søren;
Fan, Wei;
Wang, Junyi;
Zhang, Zhang;
Wang, Wen;
Kristiansen, Karsten;
Wang, Jun

Publication type:

Article

Sequence harmony: detecting functional specificity from alignments.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W495, doi. 10.1093/nar/gkm406

By:

Feenstra, K. Anton;
Pirovano, Walter;
Krab, Klaas;
Heringa, Jaap

Publication type:

Article

CanPredict: a computational tool for predicting cancer-associated missense mutations.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W595, doi. 10.1093/nar/gkm405

By:

Kaminker, Joshua S.;
Zhang, Yan;
Watanabe, Colin;
Zhang, Zemin

Publication type:

Article

Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W526, doi. 10.1093/nar/gkm401

By:

Shazman, Shula;
Celniker, Gershon;
Haber, Omer;
Glaser, Fabian;
Mandel-Gutfreund, Yael

Publication type:

Article

The SLiMDisc server: short, linear motif discovery in proteins.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W455, doi. 10.1093/nar/gkm400

By:

Davey, Norman E.;
Edwards, Richard J.;
Shields, Denis C.

Publication type:

Article

TFAM 1.0: an online tRNA function classifier.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W350, doi. 10.1093/nar/gkm393

By:

Tåquist, Helena;
Cui, Yuanyuan;
Ardell, David H.

Publication type:

Article

CodonO: codon usage bias analysis within and across genomes.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W132, doi. 10.1093/nar/gkm392

By:

Angellotti, Michael C.;
Bhuiyan, Shafquat B.;
Chen, Guorong;
Wan, Xiu-Feng

Publication type:

Article

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W345, doi. 10.1093/nar/gkm391

By:

Kong, Lei;
Zhang, Yong;
Ye, Zhi-Qiang;
Liu, Xiao-Qiao;
Zhao, Shu-Qi;
Wei, Liping;
Gao, Ge

Publication type:

Article

DOMAC: an accurate, hybrid protein domain prediction server.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W354, doi. 10.1093/nar/gkm390

By:

Cheng, Jianlin

Publication type:

Article

REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W58, doi. 10.1093/nar/gkm384

By:

Collins, Roy Eric;
Rocap, Gabrielle

Publication type:

Article

PrimerZ: streamlined primer design for promoters, exons and human SNPs.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W63, doi. 10.1093/nar/gkm383

By:

Tsai, Ming-Fang;
Lin, Yi-Jung;
Cheng, Yu-Chang;
Lee, Kuo-Hsi;
Huang, Cheng-Chih;
Chen, Yuan-Tsong;
Yao, Adam

Publication type:

Article

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W506, doi. 10.1093/nar/gkm382

By:

Stern, Adi;
Doron-Faigenboim, Adi;
Erez, Elana;
Martz, Eric;
Bacharach, Eran;
Pupko, Tal

Publication type:

Article

GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W152, doi. 10.1093/nar/gkm381

By:

Zhang, Yan;
Luoh, Shiuh-Ming;
Hon, Lawrence S.;
Baertsch, Robert;
Wood, William I.;
Zhang, Zemin

Publication type:

Article

MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W97

By:

Ou, Hong-Yu;
He, Xinyi;
Harrison, Ewan M.;
Kulasekara, Bridget R.;
Thani, Ali Bin;
Kadioglu, Aras;
Lory, Stephen;
Hinton, Jay C. D.;
Barer, Michael R.;
Deng, Zixin;
Rajakumar, Kumar

Publication type:

Article

MYBS: a comprehensive web server for mining transcription factor binding sites in yeast.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W221, doi. 10.1093/nar/gkm379

By:

Tsai, Huai-Kuang;
Chou, Meng-Yuan;
Shih, Ching-Hua;
Huang, Grace Tzu-Wei;
Chang, Tien-Hsien;
Li, Wen-Hsiung

Publication type:

Article

ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W143, doi. 10.1093/nar/gkm378

By:

Nagaraj, Shivashankar H.;
Deshpande, Nandan;
Gasser, Robin B.;
Ranganathan, Shoba

Publication type:

Article

WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W217, doi. 10.1093/nar/gkm376

By:

Romer, Katherine A.;
Kayombya, Guy-Richard;
Fraenkel, Ernest

Publication type:

Article

ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W701, doi. 10.1093/nar/gkm371

By:

Zamdborg, Leonid;
LeDuc, Richard D.;
Glowacz, Kevin J.;
Kim, Yong-Bin;
Viswanathan, Vinayak;
Spaulding, Ian T.;
Early, Bryan P.;
Bluhm, Eric J.;
Babai, Shannee;
Kelleher, Neil L.

Publication type:

Article

EVALLER: a web server for in silico assessment of potential protein allergenicity.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W694, doi. 10.1093/nar/gkm370

By:

Barrio, Alvaro Martinez;
Soeria-Atmadja, Daniel;
Nistér, Anders;
Gustafsson, Mats G.;
Hammerling, Ulf;
Bongcam-Rudloff, Erik

Publication type:

Article

ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W159, doi. 10.1093/nar/gkm369

By:

Lee, Byungwook;
Hong, Taehui;
Byun, Sang Jin;
Woo, Taeha;
Choi, Yoon Jeong

Publication type:

Article

MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W339, doi. 10.1093/nar/gkm368

By:

Jiang, Peng;
Wu, Haonan;
Wang, Wenkai;
Ma, Wei;
Sun, Xiao;
Lu, Zuhong

Publication type:

Article

FRalanyzer: a tool for functional analysis of fold-recognition sequence–structure alignments.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W499, doi. 10.1093/nar/gkm367

By:

Saini, Harpreet Kaur;
Fischer, Daniel

Publication type:

Article

FluGenome: a web tool for genotyping influenza A virus.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W275

By:

Lu, Guoqing;
Rowley, Thaine;
Garten, Rebecca;
Donis, Ruben O.

Publication type:

Article

ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W444, doi. 10.1093/nar/gkm364

By:

del Val, C.;
Ernst, P.;
Falkenhahn, M;
Fladerer, C.;
Glatting, K. H.;
Suhai, S.;
Hotz-Wagenblatt, A.

Publication type:

Article

PrDOS: prediction of disordered protein regions from amino acid sequence.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W460, doi. 10.1093/nar/gkm363

By:

Ishida, Takashi;
Kinoshita, Kengo

Publication type:

Article

Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W227, doi. 10.1093/nar/gkm362

By:

Okumura, Toshiyuki;
Makiguchi, Hiroki;
Makita, Yuko;
Yamashita, Riu;
Nakai, Kenta

Publication type:

Article

RSRE: RNA structural robustness evaluator.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W314, doi. 10.1093/nar/gkm361

By:

Shu, Wenjie;
Bo, Xiaochen;
Zheng, Zhiqiang;
Wang, Shengqi

Publication type:

Article

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W52, doi. 10.1093/nar/gkm360

By:

Grissa, Ibtissem;
Vergnaud, Gilles;
Pourcel, Christine

Publication type:

Article

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W33, doi. 10.1093/nar/gkm359

By:

Keane, Thomas M.;
Naughton, Thomas J.;
McInerney, James O.

Publication type:

Article

FLAN: a web server for influenza virus genome annotation.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W280, doi. 10.1093/nar/gkm354

By:

Bao, Yiming;
Bolotov, Pavel;
Dernovoy, Dmitry;
Kiryutin, Boris;
Tatusova, Tatiana

Publication type:

Article

iPDA: integrated protein disorder analyzer.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W465

By:

Su, Chung-Tsai;
Chen, Chien-Yu;
Hsu, Chen-Ming

Publication type:

Article

MyHits: improvements to an interactive resource for analyzing protein sequences.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W433, doi. 10.1093/nar/gkm352

By:

Pagni, Marco;
Ioannidis, Vassilios;
Cerutti, Lorenzo;
Zahn-Zabal, Monique;
Jongeneel, C. Victor;
Hau, Jörg;
Martin, Olivier;
Kuznetsov, Dmitri;
Falquet, Laurent

Publication type:

Article

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W398, doi. 10.1093/nar/gkm351

By:

Kinoshita, Kengo;
Murakami, Yoichi;
Nakamura, Haruki

Publication type:

Article

INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W633, doi. 10.1093/nar/gkm350

By:

Chen, Feng-Chi;
Chen, Chueng-Jong;
Chuang, Trees-Juen

Publication type:

Article

Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W599, doi. 10.1093/nar/gkm349

By:

Sander, Jeffry D.;
Zaback, Peter;
Joung, J. Keith;
Voytas, Daniel F.;
Dobbs, Drena

Publication type:

Article

3D-partner: a web server to infer interacting partners and binding models.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W561, doi. 10.1093/nar/gkm346

By:

Chen, Yung-Chiang;
Lo, Yu-Shu;
Hsu, Wen-Chang;
Yang, Jinn-Moon

Publication type:

Article

The Multi-Q web server for multiplexed protein quantitation.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W707

By:

Yu, Chuan-Yih;
Tsui, Yin-Hao;
Yian, Yi-Hwa;
Sung, Ting-Yi;
Hsu, Wen-Lian

Publication type:

Article

BIPASS: BioInformatics Pipeline Alternative Splicing Services.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W292, doi. 10.1093/nar/gkm344

By:

Lacroix, Zoé;
Legendre, Christophe;
Raschid, Louiqa;
Snyder, Ben

Publication type:

Article

MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W201, doi. 10.1093/nar/gkm343

By:

Schmid, Christoph D.;
Sengstag, Thierry;
Bucher, Philipp;
Delorenzi, Mauro

Publication type:

Article

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W477, doi. 10.1093/nar/gkm342

By:

Franklin, Joel;
Koehl, Patrice;
Doniach, Sebastian;
Delarue, Marc

Publication type:

Article