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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