Published in BMC Bioinformatics on October 10, 2003
Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) 31.84
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics (2009) 2.64
An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol (2006) 2.35
Quality measures for protein alignment benchmarks. Nucleic Acids Res (2010) 2.23
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res (2010) 2.05
DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics (2005) 1.87
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 comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One (2011) 1.65
How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis. BMC Genomics (2012) 1.62
Alignment of multiple protein structures based on sequence and structure features. Protein Eng Des Sel (2009) 1.43
Visualization of multiple alignments, phylogenies and gene family evolution. Nat Methods (2010) 1.34
Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0. Mol Biol Evol (2009) 1.23
PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences. Nucleic Acids Res (2010) 1.16
Accuracy of structure-based sequence alignment of automatic methods. BMC Bioinformatics (2007) 1.14
S4: structure-based sequence alignments of SCOP superfamilies. Nucleic Acids Res (2005) 1.09
A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics (2016) 1.05
A comparison of common programming languages used in bioinformatics. BMC Bioinformatics (2008) 1.04
Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinformatics (2005) 1.03
MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. BMC Bioinformatics (2012) 0.99
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep (2013) 0.97
Quantification of the variation in percentage identity for protein sequence alignments. BMC Bioinformatics (2006) 0.94
Subfamily specific conservation profiles for proteins based on n-gram patterns. BMC Bioinformatics (2008) 0.92
Alignment of helical membrane protein sequences using AlignMe. PLoS One (2013) 0.92
ccPDB: compilation and creation of data sets from Protein Data Bank. Nucleic Acids Res (2011) 0.90
SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools. BMC Bioinformatics (2006) 0.90
Protein sequence alignment with family-specific amino acid similarity matrices. BMC Res Notes (2011) 0.89
Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. BMC Bioinformatics (2008) 0.87
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts. BMC Bioinformatics (2011) 0.87
SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation. BMC Bioinformatics (2011) 0.86
Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees. Bioinformatics (2016) 0.86
An assessment of substitution scores for protein profile-profile comparison. Bioinformatics (2011) 0.85
eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities. Nucleic Acids Res (2007) 0.85
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics (2015) 0.83
Computational approaches to study the effects of small genomic variations. J Mol Model (2015) 0.81
Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. BMC Bioinformatics (2015) 0.81
Sequence alignment for molecular replacement. Acta Crystallogr D Biol Crystallogr (2007) 0.81
QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors. PLoS One (2014) 0.79
AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis. Nucleic Acids Res (2010) 0.79
Computational enzyme design approaches with significant biological outcomes: progress and challenges. Comput Struct Biotechnol J (2012) 0.78
Benchmark datasets and software for developing and testing methods for large-scale multiple sequence alignment and phylogenetic inference. PLoS Curr (2010) 0.78
FAMSA: Fast and accurate multiple sequence alignment of huge protein families. Sci Rep (2016) 0.77
Full-length structural model of RET3 and SEC21 in COPI: identification of binding sites on the appendage for accessory protein recruitment motifs. J Mol Model (2012) 0.76
Quantifying the displacement of mismatches in multiple sequence alignment benchmarks. PLoS One (2015) 0.75
Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques. Nucleic Acids Res (2012) 0.75
PnpProbs: a better multiple sequence alignment tool by better handling of guide trees. BMC Bioinformatics (2016) 0.75
MSAIndelFR: a scheme for multiple protein sequence alignment using information on indel flanking regions. BMC Bioinformatics (2015) 0.75
Improving multiple sequence alignment by using better guide trees. BMC Bioinformatics (2015) 0.75
Div-BLAST: diversification of sequence search results. PLoS One (2014) 0.75
Protein Multiple Sequence Alignment Benchmarking through Secondary Structure Prediction. Bioinformatics (2017) 0.75
ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach. BMC Bioinformatics (2014) 0.75
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol (1970) 155.96
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A (1992) 61.33
T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol (2000) 57.88
Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol (1987) 41.41
Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol (1994) 31.57
A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J Mol Biol (1987) 19.30
Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct (2000) 17.81
A tool for multiple sequence alignment. Proc Natl Acad Sci U S A (1989) 17.09
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol (1996) 15.98
Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput Appl Biosci (1993) 15.69
Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. Protein Eng (1992) 14.40
Identification of protein sequence homology by consensus template alignment. J Mol Biol (1986) 13.73
A weighting system and algorithm for aligning many phylogenetically related sequences. Comput Appl Biosci (1995) 13.48
Automatic generation of primary sequence patterns from sets of related protein sequences. Proc Natl Acad Sci U S A (1990) 12.96
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics (1999) 12.64
Exhaustive matching of the entire protein sequence database. Science (1992) 11.29
ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng (1993) 10.04
The SWISS-PROT protein sequence data bank. Nucleic Acids Res (1991) 9.45
Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci (1993) 9.38
Simultaneous comparison of three protein sequences. Proc Natl Acad Sci U S A (1985) 6.96
Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins (2000) 6.22
Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc Natl Acad Sci U S A (1996) 6.02
Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins (1992) 4.92
An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. J Mol Biol (1995) 3.74
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins (1999) 3.60
Evaluation and improvements in the automatic alignment of protein sequences. Protein Eng (1989) 3.57
Dynamic programming alignment accuracy. J Comput Biol (1998) 3.22
Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. Bioinformatics (2001) 2.92
Comparative analysis of multiple protein-sequence alignment methods. Mol Biol Evol (1994) 2.91
Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci (1994) 2.56
The structural alignment between two proteins: is there a unique answer? Protein Sci (1996) 2.50
Optimum superimposition of protein structures: ambiguities and implications. Fold Des (1996) 2.23
Protein multiple sequence alignment and flexible pattern matching. Methods Enzymol (1990) 2.11
Critical assessment of methods of protein structure prediction (CASP): round II. Proteins (1997) 2.00
Determination of reliable regions in protein sequence alignments. Protein Eng (1990) 1.66
Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J Comput Biol (1995) 1.47
Predicting reliable regions in protein sequence alignments. Bioinformatics (2002) 1.34
3Dee: a database of protein structural domains. Bioinformatics (2001) 1.33
Estimation of P-values for global alignments of protein sequences. Bioinformatics (2001) 1.31
Protein structural domains: analysis of the 3Dee domains database. Proteins (2001) 1.06
Further improvement in methods of group-to-group sequence alignment with generalized profile operations. Comput Appl Biosci (1994) 0.98
Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) 31.84
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
The Jalview Java alignment editor. Bioinformatics (2004) 21.74
Ensembl 2011. Nucleic Acids Res (2010) 14.68
Ensembl 2012. Nucleic Acids Res (2011) 14.55
The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32
Ensembl 2014. Nucleic Acids Res (2013) 12.62
Ensembl 2013. Nucleic Acids Res (2012) 11.70
Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
The Ensembl analysis pipeline. Genome Res (2004) 5.90
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res (2006) 4.64
Emerging roles of pseudokinases. Trends Cell Biol (2006) 4.48
Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA (2009) 3.87
System-wide changes to SUMO modifications in response to heat shock. Sci Signal (2009) 3.50
The African coelacanth genome provides insights into tetrapod evolution. Nature (2013) 2.78
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet (2013) 2.76
A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science (2011) 2.50
Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell (2012) 2.37
MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics (2006) 2.23
Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res (2013) 2.19
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol (2011) 2.18
Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput Biol (2009) 2.06
Regulation of the miR-212/132 locus by MSK1 and CREB in response to neurotrophins. Biochem J (2010) 1.94
PIPs: human protein-protein interaction prediction database. Nucleic Acids Res (2008) 1.91
TarO: a target optimisation system for structural biology. Nucleic Acids Res (2008) 1.89
Incorporating RNA-seq data into the zebrafish Ensembl genebuild. Genome Res (2012) 1.89
The Scottish Structural Proteomics Facility: targets, methods and outputs. J Struct Funct Genomics (2010) 1.66
Classification and functional annotation of eukaryotic protein kinases. Proteins (2007) 1.62
The phosphoproteome of bloodstream form Trypanosoma brucei, causative agent of African sleeping sickness. Mol Cell Proteomics (2009) 1.56
Characterization and prediction of protein nucleolar localization sequences. Nucleic Acids Res (2010) 1.40
The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol (2007) 1.38
Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res (2011) 1.35
Visualization of multiple alignments, phylogenies and gene family evolution. Nat Methods (2010) 1.34
Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation. Nat Struct Mol Biol (2012) 1.34
Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases. EMBO J (2009) 1.32
Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics (2007) 1.31
Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects. J Allergy Clin Immunol (2013) 1.30
Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation. Proc Natl Acad Sci U S A (2012) 1.29
PTEN protein phosphatase activity correlates with control of gene expression and invasion, a tumor-suppressing phenotype, but not with AKT activity. Sci Signal (2012) 1.15
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. Nucleic Acids Res (2007) 1.15
A normalised scale for structural genomics target ranking: the OB-Score. FEBS Lett (2006) 1.15
Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res (2008) 1.12
The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4. EMBO J (2011) 1.11
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. Bioinformatics (2008) 1.10
Haploinsufficiency for AAGAB causes clinically heterogeneous forms of punctate palmoplantar keratoderma. Nat Genet (2012) 1.08
NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. BMC Bioinformatics (2011) 1.06
The complement of protein kinases of the microsporidium Encephalitozoon cuniculi in relation to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe. BMC Genomics (2007) 1.04
Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Res (2011) 1.04
Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA. Bioinformatics (2011) 1.00
A new family of transcription factors. Development (2008) 0.98
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC Bioinformatics (2008) 0.97
Identification of a glycosylphosphatidylinositol anchor-modifying beta1-3 N-acetylglucosaminyl transferase in Trypanosoma brucei. Mol Microbiol (2008) 0.96
The kinomes of apicomplexan parasites. Microbes Infect (2012) 0.96
Quantification of the variation in percentage identity for protein sequence alignments. BMC Bioinformatics (2006) 0.94
Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. Mol Biol Cell (2010) 0.94
PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities. BMC Res Notes (2011) 0.92
Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA. PLoS Genet (2013) 0.91
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus. BMC Syst Biol (2011) 0.89
Biological units and their effect upon the properties and prediction of protein-protein interactions. J Mol Biol (2006) 0.89
Genome analysis of the unicellular green alga Chlamydomonas reinhardtii Indicates an ancient evolutionary origin for key pattern recognition and cell-signaling protein families. Genetics (2008) 0.88
Prophossi: automating expert validation of phosphopeptide-spectrum matches from tandem mass spectrometry. Bioinformatics (2010) 0.88
Increased coverage obtained by combination of methods for protein sequence database searching. Bioinformatics (2003) 0.88
Ensembl comparative genomics resources. Database (Oxford) (2016) 0.87
XANNpred: neural nets that predict the propensity of a protein to yield diffraction-quality crystals. Proteins (2011) 0.85
A comparison of SCOP and CATH with respect to domain-domain interactions. Proteins (2008) 0.85
The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation. Sci Rep (2013) 0.83
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. Nucleic Acids Res (2008) 0.82
Expression, purification, crystallization, data collection and preliminary biochemical characterization of methicillin-resistant Staphylococcus aureus Sar2028, an aspartate/tyrosine/phenylalanine pyridoxal-5'-phosphate-dependent aminotransferase. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 0.81
Purification, crystallization and data collection of methicillin-resistant Staphylococcus aureus Sar2676, a pantothenate synthetase. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 0.81
Elevated O-GlcNAc levels activate epigenetically repressed genes and delay mouse ESC differentiation without affecting naïve to primed cell transition. Stem Cells (2014) 0.80
Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet (2016) 0.78
Computational approaches to selecting and optimising targets for structural biology. Methods (2011) 0.77
Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA (2016) 0.76
PNAC: a protein nucleolar association classifier. BMC Genomics (2011) 0.76
Visual representation of database search results: the RHIMS Plot. Bioinformatics (2003) 0.75