Wednesday, June 29, 2011

Nucleic Acids Research

Articles

The 2011 bioinformatics links directory update: more resources, tools and databases and features to empower the bioinformatics community

Michelle D. Brazas, David S. Yim, Joseph T. Yamada, and B. F. Francis Ouellette
Nucl. Acids Res. 2011 39:W3-W7.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W3

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences

Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon
Nucl. Acids Res. 2011 39:W8-W12.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W8

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

Paolo Di Tommaso, Sebastien Moretti, Ioannis Xenarios, Miquel Orobitg, Alberto Montanyola, Jia-Ming Chang, Jean-François Taly, and Cedric Notredame
Nucl. Acids Res. 2011 39:W13-W17.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W13

iPBA: a tool for protein structure comparison using sequence alignment strategies

Jean-Christophe Gelly, Agnel Praveen Joseph, Narayanaswamy Srinivasan, and Alexandre G. de Brevern
Nucl. Acids Res. 2011 39:W18-W23.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W18

CLICK—topology-independent comparison of biomolecular 3D structures

M. N. Nguyen, K. P. Tan, and M. S. Madhusudhan
Nucl. Acids Res. 2011 39:W24-W28.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W24

HMMER web server: interactive sequence similarity searching

Robert D. Finn, Jody Clements, and Sean R. Eddy
Nucl. Acids Res. 2011 39:W29-W37.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W29

FFAS server: novel features and applications

Lukasz Jaroszewski, Zhanwen Li, Xiao-hui Cai, Christoph Weber, and Adam Godzik
Nucl. Acids Res. 2011 39:W38-W44.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W38

R3D-BLAST: a search tool for similar RNA 3D substructures

Yun-Chen Liu, Chung-Han Yang, Kun-Tze Chen, Jyun-Rong Wang, Mei-Ling Cheng, Jen-Chun Chung, Hsien-Tai Chiu, and Chin Lung Lu
Nucl. Acids Res. 2011 39:W45-W49.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W45

WebFR3D—a server for finding, aligning and analyzing recurrent RNA 3D motifs

Anton I. Petrov, Craig L. Zirbel, and Neocles B. Leontis
Nucl. Acids Res. 2011 39:W50-W55.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W50

SLiMSearch 2.0: biological context for short linear motifs in proteins

Norman E. Davey, Niall J. Haslam, Denis C. Shields, and Richard J. Edwards
Nucl. Acids Res. 2011 39:W56-W60.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W56

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design

Lars Rønn Olsen, Niels Bjørn Hansen, Mads Tvillinggaard Bonde, Hans Jasper Genee, Dorte Koefoed Holm, Simon Carlsen, Bjarne Gram Hansen, Kiran Raosaheb Patil, Uffe Hasbro Mortensen, and Rasmus Wernersson
Nucl. Acids Res. 2011 39:W61-W67.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W61

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

Christophe Blanchet, Marco Pasi, Krystyna Zakrzewska, and Richard Lavery
Nucl. Acids Res. 2011 39:W68-W73.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W68

ConTra v2: a tool to identify transcription factor binding sites across species, update 2011

Stefan Broos, Paco Hulpiau, Jeroen Galle, Bart Hooghe, Frans Van Roy, and Pieter De Bleser
Nucl. Acids Res. 2011 39:W74-W78.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W74

Genome surveyor 2.0: cis-regulatory analysis in Drosophila

Majid Kazemian, Michael H. Brodsky, and Saurabh Sinha
Nucl. Acids Res. 2011 39:W79-W85.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W79

RSAT 2011: regulatory sequence analysis tools

Morgane Thomas-Chollier, Matthieu Defrance, Alejandra Medina-Rivera, Olivier Sand, Carl Herrmann, Denis Thieffry, and Jacques van Helden
Nucl. Acids Res. 2011 39:W86-W91.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W86

The RNAmute web server for the mutational analysis of RNA secondary structures

Alexander Churkin, Idan Gabdank, and Danny Barash
Nucl. Acids Res. 2011 39:W92-W99.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W92

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences

Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, and Kiyoshi Asai
Nucl. Acids Res. 2011 39:W100-W106.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W100

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

Stefan E. Seemann, Peter Menzel, Rolf Backofen, and Jan Gorodkin
Nucl. Acids Res. 2011 39:W107-W111.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W107

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments

Mario Fasold, David Langenberger, Hans Binder, Peter F. Stadler, and Steve Hoffmann
Nucl. Acids Res. 2011 39:W112-W117.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W112

ncFANs: a web server for functional annotation of long non-coding RNAs

Qi Liao, Hui Xiao, Dechao Bu, Chaoyong Xie, Ruoyu Miao, Haitao Luo, Guoguang Zhao, Kuntao Yu, Haitao Zhao, Geir Skogerbø, Runsheng Chen, Zhongdao Wu, Changning Liu, and Yi Zhao
Nucl. Acids Res. 2011 39:W118-W124.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W118

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling

Christopher L. Plaisier, J. Christopher Bare, and Nitin S. Baliga
Nucl. Acids Res. 2011 39:W125-W131.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W125

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

Michael Hackenberg, Naiara Rodríguez-Ezpeleta, and Ana M. Aransay
Nucl. Acids Res. 2011 39:W132-W138.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W132

mirAct: a web tool for evaluating microRNA activity based on gene expression data

Zhi Liang, Hong Zhou, Zongxiao He, Haoran Zheng, and Jiarui Wu
Nucl. Acids Res. 2011 39:W139-W144.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W139

DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association

Manolis Maragkakis, Thanasis Vergoulis, Panagiotis Alexiou, Martin Reczko, Kyriaki Plomaritou, Mixail Gousis, Kornilios Kourtis, Nectarios Koziris, Theodore Dalamagas, and Artemis G. Hatzigeorgiou
Nucl. Acids Res. 2011 39:W145-W148.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W145

RNApredator: fast accessibility-based prediction of sRNA targets

Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, and Ivo L. Hofacker
Nucl. Acids Res. 2011 39:W149-W154.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W149

psRNATarget: a plant small RNA target analysis server

Xinbin Dai and Patrick Xuechun Zhao
Nucl. Acids Res. 2011 39:W155-W159.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W155

corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs

Edmund Lam, Alfred Kam, and Jérôme Waldispühl
Nucl. Acids Res. 2011 39:W160-W166.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W160

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map

Elina Tjioe, Keren Lasker, Ben Webb, Haim J. Wolfson, and Andrej Sali
Nucl. Acids Res. 2011 39:W167-W170.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W167

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

Daniel B. Roche, Maria T. Buenavista, Stuart J. Tetchner, and Liam J. McGuffin
Nucl. Acids Res. 2011 39:W171-W176.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W171

KINARI-Web: a server for protein rigidity analysis

Naomi Fox, Filip Jagodzinski, Yang Li, and Ileana Streinu
Nucl. Acids Res. 2011 39:W177-W183.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W177

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

Frédéric Poitevin, Henri Orland, Sebastian Doniach, Patrice Koehl, and Marc Delarue
Nucl. Acids Res. 2011 39:W184-W189.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W184

CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs

Ian Walsh, Alberto J. M. Martin, Tomàs Di Domenico, Alessandro Vullo, Gianluca Pollastri, and Silvio C. E. Tosatto
Nucl. Acids Res. 2011 39:W190-W196.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W190

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences

Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Andrea Zauli, Ivan Rossi, and Rita Casadio
Nucl. Acids Res. 2011 39:W197-W202.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W197

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops

Leslie Regad, Adrien Saladin, Julien Maupetit, Colette Geneix, and Anne-Claude Camproux
Nucl. Acids Res. 2011 39:W203-W209.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W203

The FALC-Loop web server for protein loop modeling

Junsu Ko, Dongseon Lee, Hahnbeom Park, Evangelos A. Coutsias, Julian Lee, and Chaok Seok
Nucl. Acids Res. 2011 39:W210-W214.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W210

SDM—a server for predicting effects of mutations on protein stability and malfunction

Catherine L. Worth, Robert Preissner, and Tom L. Blundell
Nucl. Acids Res. 2011 39:W215-W222.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W215

GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing

Alexander A. Kantardjiev
Nucl. Acids Res. 2011 39:W223-W228.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W223

PRUNE and PROBE—two modular web services for protein–protein docking

Pralay Mitra and Debnath Pal
Nucl. Acids Res. 2011 39:W229-W234.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W229

firestar—advances in the prediction of functionally important residues

Gonzalo Lopez, Paolo Maietta, Jose Manuel Rodriguez, Alfonso Valencia, and Michael L. Tress
Nucl. Acids Res. 2011 39:W235-W241.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W235

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Kuan Pern Tan, Raghavan Varadarajan, and M. S. Madhusudhan
Nucl. Acids Res. 2011 39:W242-W248.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W242

Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

Nir London, Barak Raveh, Eyal Cohen, Guy Fathi, and Ora Schueler-Furman
Nucl. Acids Res. 2011 39:W249-W253.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W249

PAComplex: a web server to infer peptide antigen families and binding models from TCR–pMHC complexes

I-Hsin Liu, Yu-Shu Lo, and Jinn-Moon Yang
Nucl. Acids Res. 2011 39:W254-W260.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W254

Swimming into peptidomimetic chemical space using pepMMsMIMIC

Matteo Floris, Joel Masciocchi, Marco Fanton, and Stefano Moro
Nucl. Acids Res. 2011 39:W261-W269.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W261

SwissDock, a protein-small molecule docking web service based on EADock DSS

Aurélien Grosdidier, Vincent Zoete, and Olivier Michielin
Nucl. Acids Res. 2011 39:W270-W277.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W270

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures

Luca Parca, Iolanda Mangone, Pier Federico Gherardini, Gabriele Ausiello, and Manuela Helmer-Citterich
Nucl. Acids Res. 2011 39:W278-W282.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W278

PredUs: a web server for predicting protein interfaces using structural neighbors

Qiangfeng Cliff Zhang, Lei Deng, Markus Fisher, Jihong Guan, Barry Honig, and Donald Petrey
Nucl. Acids Res. 2011 39:W283-W287.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W283

MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence

Andrea Passerini, Marco Lippi, and Paolo Frasconi
Nucl. Acids Res. 2011 39:W288-W292.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W288

RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology

Aleksandra Gruca, Marek Sikora, and Andrzej Polanski
Nucl. Acids Res. 2011 39:W293-W301.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W293

ADGO 2.0: interpreting microarray data and list of genes using composite annotations

Sang-Mun Chi, Jin Kim, Seon-Young Kim, and Dougu Nam
Nucl. Acids Res. 2011 39:W302-W306.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W302

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

Jüri Reimand, Tambet Arak, and Jaak Vilo
Nucl. Acids Res. 2011 39:W307-W315.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W307

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, and Liping Wei
Nucl. Acids Res. 2011 39:W316-W322.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W316

BioProfiling.de: analytical web portal for high-throughput cell biology

Alexey V. Antonov
Nucl. Acids Res. 2011 39:W323-W327.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W323

AnnotQTL: a new tool to gather functional and comparative information on a genomic region

F. Lecerf, A. Bretaudeau, O. Sallou, C. Desert, Y. Blum, S. Lagarrigue, and O. Demeure
Nucl. Acids Res. 2011 39:W328-W333.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W328

PINTA: a web server for network-based gene prioritization from expression data

Daniela Nitsch, Léon-Charles Tranchevent, Joana P. Gonçalves, Josef Korbinian Vogt, Sara C. Madeira, and Yves Moreau
Nucl. Acids Res. 2011 39:W334-W338.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W334

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Eriko Takano, and Rainer Breitling
Nucl. Acids Res. 2011 39:W339-W346.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W339

PHAST: A Fast Phage Search Tool

You Zhou, Yongjie Liang, Karlene H. Lynch, Jonathan J. Dennis, and David S. Wishart
Nucl. Acids Res. 2011 39:W347-W352.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W347

GCView: the genomic context viewer for protein homology searches

Iwan Grin and Dirk Linke
Nucl. Acids Res. 2011 39:W353-W356.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W353

MarkUs: a server to navigate sequence–structure–function space

Markus Fischer, Qiangfeng Cliff Zhang, Fabian Dey, Brian Y. Chen, Barry Honig, and Donald Petrey
Nucl. Acids Res. 2011 39:W357-W361.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W357

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity

Marc Röttig, Marnix H. Medema, Kai Blin, Tilmann Weber, Christian Rausch, and Oliver Kohlbacher
Nucl. Acids Res. 2011 39:W362-W367.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W362

PILGRM: an interactive data-driven discovery platform for expert biologists

Casey S. Greene and Olga G. Troyanskaya
Nucl. Acids Res. 2011 39:W368-W374.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W368

MemPype: a pipeline for the annotation of eukaryotic membrane proteins

Andrea Pierleoni, Valentina Indio, Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, and Rita Casadio
Nucl. Acids Res. 2011 39:W375-W380.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W375

PepServe: a web server for peptide analysis, clustering and visualization

Anastasia Alexandridou, Nikolas Dovrolis, George Th. Tsangaris, Konstantina Nikita, and George Spyrou
Nucl. Acids Res. 2011 39:W381-W384.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W381

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

H. B. Rao, F. Zhu, G. B. Yang, Z. R. Li, and Y. Z. Chen
Nucl. Acids Res. 2011 39:W385-W390.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W385

CENTDIST: discovery of co-associated factors by motif distribution

Zhizhuo Zhang, Cheng Wei Chang, Wan Ling Goh, Wing-Kin Sung, and Edwin Cheung
Nucl. Acids Res. 2011 39:W391-W399.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W391

GLAMM: Genome-Linked Application for Metabolic Maps

John T. Bates, Dylan Chivian, and Adam P. Arkin
Nucl. Acids Res. 2011 39:W400-W405.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W400

The University of Minnesota Pathway Prediction System: multi-level prediction and visualization

Junfeng Gao, Lynda B. M. Ellis, and Lawrence P. Wackett
Nucl. Acids Res. 2011 39:W406-W411.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W406

iPath2.0: interactive pathway explorer

Takuji Yamada, Ivica Letunic, Shujiro Okuda, Minoru Kanehisa, and Peer Bork
Nucl. Acids Res. 2011 39:W412-W415.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W412

mirConnX: condition-specific mRNA-microRNA network integrator

Grace T. Huang, Charalambos Athanassiou, and Panayiotis V. Benos
Nucl. Acids Res. 2011 39:W416-W423.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W416

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

Alex Lan, Ilan Y. Smoly, Guy Rapaport, Susan Lindquist, Ernest Fraenkel, and Esti Yeger-Lotem
Nucl. Acids Res. 2011 39:W424-W429.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W424

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor

Jing Qin, Mulin Jun Li, Panwen Wang, Michael Q. Zhang, and Junwen Wang
Nucl. Acids Res. 2011 39:W430-W436.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W430

ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework

Kunlin Zhang, Suhua Chang, Sijia Cui, Liyuan Guo, Liuyan Zhang, and Jing Wang
Nucl. Acids Res. 2011 39:W437-W443.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W437

SNPsyn: detection and exploration of SNP–SNP interactions

Tomaz Curk, Gregor Rot, and Blaz Zupan
Nucl. Acids Res. 2011 39:W444-W449.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W444

CoPub update: CoPub 5.0 a text mining system to answer biological questions

Wilco W. M. Fleuren, Stefan Verhoeven, Raoul Frijters, Bart Heupers, Jan Polman, René van Schaik, Jacob de Vlieg, and Wynand Alkema
Nucl. Acids Res. 2011 39:W450-W454.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W450

Génie: literature-based gene prioritization at multi genomic scale

Jean-Fred Fontaine, Florian Priller, Adriano Barbosa-Silva, and Miguel A. Andrade-Navarro
Nucl. Acids Res. 2011 39:W455-W461.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W455

BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature

Moushumi Sen Sarma, David Arcoleo, Radhika S. Khetani, Brant Chee, Xu Ling, Xin He, Jing Jiang, Qiaozhu Mei, ChengXiang Zhai, and Bruce Schatz
Nucl. Acids Res. 2011 39:W462-W469.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W462

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

Rubén Sánchez, François Serra, Joaquín Tárraga, Ignacio Medina, José Carbonell, Luis Pulido, Alejandro de María, Salvador Capella-Gutíerrez, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, and Hernán Dopazo
Nucl. Acids Res. 2011 39:W470-W474.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W470

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

Ivica Letunic and Peer Bork
Nucl. Acids Res. 2011 39:W475-W478.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W475

PhyleasProg: a user-oriented web server for wide evolutionary analyses

Joël Busset, Cédric Cabau, Camille Meslin, and Géraldine Pascal
Nucl. Acids Res. 2011 39:W479-W485.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W479

ChemMine tools: an online service for analyzing and clustering small molecules

Tyler W. H. Backman, Yiqun Cao, and Thomas Girke
Nucl. Acids Res. 2011 39:W486-W491.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W486

DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical–protein interactome

Heng Luo, Jian Chen, Leming Shi, Mike Mikailov, Huang Zhu, Kejian Wang, Lin He, and Lun Yang
Nucl. Acids Res. 2011 39:W492-W498.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W492

Detecting selection in immunoglobulin sequences

Mohamed Uduman, Gur Yaari, Uri Hershberg, Jacob A. Stern, Mark J. Shlomchik, and Steven H. Kleinstein
Nucl. Acids Res. 2011 39:W499-W504.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W499

ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry

Manor Askenazi and Michal Linial
Nucl. Acids Res. 2011 39:W505-W510.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W505

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

Enguerran Vanquelef, Sabrina Simon, Gaelle Marquant, Elodie Garcia, Geoffroy Klimerak, Jean Charles Delepine, Piotr Cieplak, and François-Yves Dupradeau
Nucl. Acids Res. 2011 39:W511-W517.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W511

CoMet—a web server for comparative functional profiling of metagenomes

Thomas Lingner, Kathrin Petra Aßhauer, Fabian Schreiber, and Peter Meinicke
Nucl. Acids Res. 2011 39:W518-W523.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W518

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

Jose M. Muiño, Marlous Hoogstraat, Roeland C. H. J. van Ham, and Aalt D. J. van Dijk
Nucl. Acids Res. 2011 39:W524-W527.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W524

The BioExtract Server: a web-based bioinformatic workflow platform

Carol M. Lushbough, Douglas M. Jennewein, and Volker P. Brendel
Nucl. Acids Res. 2011 39:W528-W532.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W528


Web Services

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

Norio Kobayashi, Manabu Ishii, Satoshi Takahashi, Yoshiki Mochizuki, Akihiro Matsushima, and Tetsuro Toyoda
Nucl. Acids Res. 2011 39:W533-W540.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W533

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

Patricia L. Whetzel, Natalya F. Noy, Nigam H. Shah, Paul R. Alexander, Csongor Nyulas, Tania Tudorache, and Mark A. Musen
Nucl. Acids Res. 2011 39:W541-W545.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W541

The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences

Corin Yeats, Jonathan Lees, Phil Carter, Ian Sillitoe, and Christine Orengo
Nucl. Acids Res. 2011 39:W546-W550.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W546


Stand Alone Programs

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing

Pavlo Lutsik, Lars Feuerbach, Julia Arand, Thomas Lengauer, Jörn Walter, and Christoph Bock
Nucl. Acids Res. 2011 39:W551-W556.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W551

HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies

Jong Hyun Kim, Woo-Cheol Kim, Lei M. Li, and Sanghyun Park
Nucl. Acids Res. 2011 39:W557-W561.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W557

PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies

Hugo López-Fernández, Daniel Glez-Peña, Miguel Reboiro-Jato, Gonzalo Gómez-López, David G. Pisano, and Florentino Fdez-Riverola
Nucl. Acids Res. 2011 39:W562-W566.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W562

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

Ji Qi and Fangqing Zhao
Nucl. Acids Res. 2011 39:W567-W575.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W567

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