Published in J Mol Biol on July 02, 2004
MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol (2013) 34.34
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res (2008) 19.09
PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 7.16
Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol (2007) 4.88
M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res (2006) 4.53
Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods. Nucleic Acids Res (2006) 4.00
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res (2006) 3.76
R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res (2008) 2.69
Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics (2009) 2.64
Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol (2008) 2.41
VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Res (2008) 2.38
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res (2010) 2.05
Predicting PDZ domain-peptide interactions from primary sequences. Nat Biotechnol (2008) 1.86
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res (2006) 1.85
A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One (2011) 1.65
PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 1.58
RaptorX: exploiting structure information for protein alignment by statistical inference. Proteins (2011) 1.55
Gene and genome duplication in Acanthamoeba polyphaga Mimivirus. J Virol (2005) 1.30
THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves. Nat Struct Mol Biol (2009) 1.27
Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2010) 1.26
Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci (2006) 1.26
Genetic isolation and characterization of a splicing mutant of zebrafish dystrophin. Hum Mol Genet (2008) 1.23
PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res (2007) 1.20
Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families. PLoS Comput Biol (2010) 1.19
PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL. BMC Bioinformatics (2012) 1.16
The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR/Cas system. J Mol Biol (2010) 1.16
Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud. Bioinformatics (2010) 1.15
Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Nat Protoc (2011) 1.14
Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol (2007) 1.14
Protein structure alignment beyond spatial proximity. Sci Rep (2013) 1.13
Vertebrate vitellogenin gene duplication in relation to the "3R hypothesis": correlation to the pelagic egg and the oceanic radiation of teleosts. PLoS One (2007) 1.11
S4: structure-based sequence alignments of SCOP superfamilies. Nucleic Acids Res (2005) 1.09
Solution structure and phylogenetics of Prod1, a member of the three-finger protein superfamily implicated in salamander limb regeneration. PLoS One (2009) 1.08
Involvement of the cytokine MIF in the snail host immune response to the parasite Schistosoma mansoni. PLoS Pathog (2010) 1.07
Hormone-activated estrogen receptors in annelid invertebrates: implications for evolution and endocrine disruption. Endocrinology (2008) 1.04
Module evolution and substrate specificity of fungal nonribosomal peptide synthetases involved in siderophore biosynthesis. BMC Evol Biol (2008) 1.02
Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions. BMC Bioinformatics (2007) 1.01
Accessible high-throughput virtual screening molecular docking software for students and educators. PLoS Comput Biol (2012) 1.01
Novel cargo-binding site in the beta and delta subunits of coatomer. J Cell Biol (2007) 1.00
Structure of the Murray Valley encephalitis virus RNA helicase at 1.9 Angstrom resolution. Protein Sci (2007) 0.98
Structural basis for promiscuity and specificity during Candida glabrata invasion of host epithelia. Proc Natl Acad Sci U S A (2012) 0.97
MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. Nucleic Acids Res (2005) 0.97
Large-scale modelling of the divergent spectrin repeats in nesprins: giant modular proteins. PLoS One (2013) 0.95
Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames). BMC Struct Biol (2009) 0.95
Accuracy analysis of multiple structure alignments. Protein Sci (2009) 0.95
Structure of the Triatoma virus capsid. Acta Crystallogr D Biol Crystallogr (2013) 0.93
Improving model construction of profile HMMs for remote homology detection through structural alignment. BMC Bioinformatics (2007) 0.90
Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Res (2008) 0.89
Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. J Biol Chem (2012) 0.89
Computational and experimental analyses of mammalian arylamine N-acetyltransferase structure and function. Drug Metab Dispos (2007) 0.87
Mechanism of tetracycline resistance by ribosomal protection protein Tet(O). Nat Commun (2013) 0.86
Two exo-beta-D-glucosaminidases/exochitosanases from actinomycetes define a new subfamily within family 2 of glycoside hydrolases. Biochem J (2006) 0.85
Ser80Ile mutation and a concurrent Pro25Leu variant of the VHL gene in an extended Hungarian von Hippel-Lindau family. BMC Med Genet (2008) 0.85
Structural descriptor database: a new tool for sequence-based functional site prediction. BMC Bioinformatics (2008) 0.84
Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE. BMC Genomics (2007) 0.84
Crystal structure of Mycobacterium tuberculosis zinc-dependent metalloprotease-1 (Zmp1), a metalloprotease involved in pathogenicity. J Biol Chem (2011) 0.84
Mutagenesis of non-conserved active site residues improves the activity and narrows the specificity of human thymidine kinase 2. Biochem Biophys Res Commun (2007) 0.83
Structural Hot Spots Determine Functional Diversity of the Candida glabrata Epithelial Adhesin Family. J Biol Chem (2015) 0.82
Discovery of an orthoreovirus in the aborted fetus of a Steller sea lion (Eumetopias jubatus). J Gen Virol (2011) 0.81
Evolutionary inaccuracy of pairwise structural alignments. Bioinformatics (2012) 0.81
In Silico screening on the three-dimensional model of the Plasmodium vivax SUB1 protease leads to the validation of a novel anti-parasite compound. J Biol Chem (2013) 0.81
Sequence alignment for molecular replacement. Acta Crystallogr D Biol Crystallogr (2007) 0.81
PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. Nucleic Acids Res (2016) 0.81
Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis. Brief Bioinform (2008) 0.80
Evolution of cyclic amidohydrolases: a highly diversified superfamily. J Mol Evol (2013) 0.80
The dissemination of C10 cysteine protease genes in Bacteroides fragilis by mobile genetic elements. BMC Microbiol (2010) 0.79
Refinement by shifting secondary structure elements improves sequence alignments. Proteins (2015) 0.79
AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis. Nucleic Acids Res (2010) 0.79
Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost. BMC Bioinformatics (2006) 0.79
Structure of the first PDZ domain of human PSD-93. Acta Crystallogr Sect F Struct Biol Cryst Commun (2009) 0.79
QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors. PLoS One (2014) 0.79
Evidence for a Golgi-to-endosome protein sorting pathway in Plasmodium falciparum. PLoS One (2014) 0.78
Monoamine neurotransmitters as substrates for novel tick sulfotransferases, homology modeling, molecular docking, and enzyme kinetics. ACS Chem Biol (2010) 0.78
Accommodation of profound sequence differences at the interfaces of eubacterial RNA polymerase multi-protein assembly. Bioinformation (2012) 0.78
LYRA, a webserver for lymphocyte receptor structural modeling. Nucleic Acids Res (2015) 0.78
An automatic method for assessing structural importance of amino acid positions. BMC Struct Biol (2009) 0.78
Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors. PeerJ (2015) 0.78
Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach. Bioinformatics (2004) 0.78
New methods for inferring population dynamics from microbial sequences. Infect Genet Evol (2006) 0.77
Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment. BMC Bioinformatics (2012) 0.77
Robustness of Helicobacter pylori infection conferred by context-variable redundancy among cysteine-rich paralogs. PLoS One (2013) 0.77
Comprehensive comparison of graph based multiple protein sequence alignment strategies. BMC Bioinformatics (2012) 0.77
PRIMO: An Interactive Homology Modeling Pipeline. PLoS One (2016) 0.76
From local structure to a global framework: recognition of protein folds. J R Soc Interface (2014) 0.76
Structure of flap endonuclease 1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus. Acta Crystallogr Sect F Struct Biol Cryst Commun (2011) 0.76
The role of a topologically conserved isoleucine in glutathione transferase structure, stability and function. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 0.76
STRIKE: evaluation of protein MSAs using a single 3D structure. Bioinformatics (2011) 0.75
3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale. Database (Oxford) (2016) 0.75
Biochemical and structural investigations on phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis. PLoS One (2017) 0.75
Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques. Nucleic Acids Res (2012) 0.75
Computational pipeline to identify and characterize functional mutations in ornithine transcarbamylase deficiency. 3 Biotech (2014) 0.75
Exploring Mouse Protein Function via Multiple Approaches. PLoS One (2016) 0.75
Proteoliposomal formulations of an HIV-1 gp41-based miniprotein elicit a lipid-dependent immunodominant response overlapping the 2F5 binding motif. Sci Rep (2017) 0.75
Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res (2003) 38.75
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol (2011) 28.61
The 1.2-megabase genome sequence of Mimivirus. Science (2004) 8.37
Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet (2006) 6.32
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet (2008) 5.23
A genome-wide perspective of genetic variation in human metabolism. Nat Genet (2009) 5.00
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics (2003) 4.88
Single mimivirus particles intercepted and imaged with an X-ray laser. Nature (2011) 4.63
M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res (2006) 4.53
Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS One (2008) 3.94
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics (2006) 3.31
Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science (2013) 2.98
Reductive genome evolution from the mother of Rickettsia. PLoS Genet (2007) 2.87
Between-group analysis of microarray data. Bioinformatics (2002) 2.71
R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res (2008) 2.69
Discovery of sexual dimorphisms in metabolic and genetic biomarkers. PLoS Genet (2011) 2.68
MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics (2005) 2.66
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res (2004) 2.50
Novel biomarkers for pre-diabetes identified by metabolomics. Mol Syst Biol (2012) 2.39
Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. Proc Natl Acad Sci U S A (2011) 2.34
Analysis and comparison of benchmarks for multiple sequence alignment. In Silico Biol (2006) 2.33
Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol (2010) 2.15
Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol Biol (2014) 2.11
Multiple sequence alignments. Curr Opin Struct Biol (2005) 2.05
Mimivirus and the emerging concept of "giant" virus. Virus Res (2006) 1.98
Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc Natl Acad Sci U S A (2014) 1.95
Mimivirus and its virophage. Annu Rev Genet (2009) 1.93
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics (2003) 1.93
CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res (2004) 1.91
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res (2007) 1.84
A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet (2011) 1.83
Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome. Genome Res (2003) 1.80
Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products. J Virol (2006) 1.76
Bioinformatics analysis of targeted metabolomics--uncovering old and new tales of diabetic mice under medication. Endocrinology (2008) 1.75
Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J Struct Funct Genomics (2003) 1.70
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. Genome Res (2010) 1.67
The dynamic range of the human metabolome revealed by challenges. FASEB J (2012) 1.61
Differences between human plasma and serum metabolite profiles. PLoS One (2011) 1.61
Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival. PLoS One (2009) 1.55
Mimivirus: the emerging paradox of quasi-autonomous viruses. Trends Genet (2010) 1.54
Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis. BMC Bioinformatics (2005) 1.54
The polyadenylation site of Mimivirus transcripts obeys a stringent 'hairpin rule'. Genome Res (2009) 1.53
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMC Syst Biol (2011) 1.52
Metabolomic markers reveal novel pathways of ageing and early development in human populations. Int J Epidemiol (2013) 1.48
Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis. Nucleic Acids Res (2004) 1.47
Set1 is required for meiotic S-phase onset, double-strand break formation and middle gene expression. EMBO J (2004) 1.46
Co-regulation of Gremlin and Notch signalling in diabetic nephropathy. Biochim Biophys Acta (2007) 1.44
Biomarkers for type 2 diabetes and impaired fasting glucose using a nontargeted metabolomics approach. Diabetes (2013) 1.44
Mouse phenotyping. Methods (2010) 1.43
Mining the unknown: a systems approach to metabolite identification combining genetic and metabolic information. PLoS Genet (2012) 1.41
Metabolic profiling reveals distinct variations linked to nicotine consumption in humans--first results from the KORA study. PLoS One (2008) 1.40
A multivariate analysis approach to the integration of proteomic and gene expression data. Proteomics (2007) 1.39
metaP-server: a web-based metabolomics data analysis tool. J Biomed Biotechnol (2010) 1.38
Temporal change in gene expression in the rat dentate gyrus following passive avoidance learning. J Neurochem (2007) 1.37
Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer. Clin Cancer Res (2008) 1.34
Human serum metabolic profiles are age dependent. Aging Cell (2012) 1.34
Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. Proc Natl Acad Sci U S A (2013) 1.32
Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses. Mol Cell Proteomics (2007) 1.31
Influence of acute phytochemical intake on human urinary metabolomic profiles. Am J Clin Nutr (2007) 1.29
Structural and functional properties of genes involved in human cancer. BMC Genomics (2006) 1.29
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Res (2006) 1.29
Mimivirus and Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. J Invertebr Pathol (2009) 1.29
GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res (2013) 1.28
Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. Opt Express (2011) 1.27
Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits. Hum Mol Genet (2013) 1.23
Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing. Virol J (2011) 1.20
MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res (2010) 1.19
High TCR diversity ensures optimal function and homeostasis of Foxp3+ regulatory T cells. Eur J Immunol (2011) 1.19
CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer. Int J Cancer (2007) 1.17
Questionnaire-based self-reported nutrition habits associate with serum metabolism as revealed by quantitative targeted metabolomics. Eur J Epidemiol (2010) 1.17
Evaluation of iterative alignment algorithms for multiple alignment. Bioinformatics (2004) 1.14
Targeted metabolomics profiles are strongly correlated with nutritional patterns in women. Metabolomics (2012) 1.13
Protein coding palindromes are a unique but recurrent feature in Rickettsia. Genome Res (2002) 1.13
Serum metabolite concentrations and decreased GFR in the general population. Am J Kidney Dis (2012) 1.12
Regulation of the hypoxic response in Candida albicans. Eukaryot Cell (2010) 1.11
Making automated multiple alignments of very large numbers of protein sequences. Bioinformatics (2013) 1.11
Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response. Expert Opin Biol Ther (2005) 1.10
Integrating transcription factor binding site information with gene expression datasets. Bioinformatics (2006) 1.10
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. BMC Genomics (2011) 1.10
Conformational flexibility of Mycobacterium tuberculosis thioredoxin reductase: crystal structure and normal-mode analysis. Acta Crystallogr D Biol Crystallogr (2005) 1.09
The copper regulon of the human fungal pathogen Cryptococcus neoformans H99. Mol Microbiol (2011) 1.08
Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis. Virology (2012) 1.08
R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res (2008) 1.07
Correlation between biofilm formation and the hypoxic response in Candida parapsilosis. Eukaryot Cell (2009) 1.06
Genomics of Megavirus and the elusive fourth domain of Life. Commun Integr Biol (2012) 1.06
From extraordinary endocytobionts to pandoraviruses. Comment on Scheid et al.: Some secrets are revealed: parasitic keratitis amoebae as vectors of the scarcely described pandoraviruses to humans. Parasitol Res (2014) 1.06
MassTRIX reloaded: combined analysis and visualization of transcriptome and metabolome data. PLoS One (2012) 1.06
Childhood obesity is associated with changes in the serum metabolite profile. Obes Facts (2012) 1.05
miR-187 is an independent prognostic factor in breast cancer and confers increased invasive potential in vitro. Clin Cancer Res (2012) 1.04
Body fat free mass is associated with the serum metabolite profile in a population-based study. PLoS One (2012) 1.04
Metabolomic profiles indicate distinct physiological pathways affected by two loci with major divergent effect on Bos taurus growth and lipid deposition. Physiol Genomics (2010) 1.04