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Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments

https://doi.org/10.1093/nar/gkg522
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1001/jama.290.24.3255-aopenalex-snapshot
Bioinformatics for Dummies
inferredcites →https://doi.org/10.1006/jmbi.1999.3091openalex-snapshot
Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von Heijne
inferredcites →https://doi.org/10.1006/jmbi.2000.4042openalex-snapshot
T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1006/mpev.2000.0785openalex-snapshot
Multiple Sequence Alignment in Phylogenetic Analysis
inferredcites →https://doi.org/10.1016/0196-8858(91)90017-dopenalex-snapshot
A time-efficient, linear-space local similarity algorithm
inferredcites →https://doi.org/10.1016/s0014-5793(02)03189-7openalex-snapshot
Quality assessment of multiple alignment programs
inferredcites →https://doi.org/10.1089/152791602317250397openalex-snapshot
Bioinformatics: Sequence, Structure and Databanks
inferredcites →https://doi.org/10.1093/bioinformatics/14.5.407openalex-snapshot
COFFEE: an objective function for multiple sequence alignments.
inferredcites →https://doi.org/10.1093/nar/22.22.4673openalex-snapshot
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
inferredcites →https://doi.org/10.1093/nar/24.1.189openalex-snapshot
The PROSITE database, its status in 1995
inferredcites →https://doi.org/10.1093/nar/29.1.55openalex-snapshot
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3
inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
inferredcites →https://doi.org/10.1093/nar/gkf493openalex-snapshot
Human non-synonymous SNPs: server and survey
inferredcites →https://doi.org/10.1093/nar/gkg046openalex-snapshot
The InterPro Database, 2003 brings increased coverage and new features
inferredcites →https://doi.org/10.1093/oso/9780199637911.003.0003openalex-snapshot
Multiple alignments for structural, functional, or phylogenetic analyses of homologous sequences
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1101/gr.212802openalex-snapshot
Accounting for Human Polymorphisms Predicted to Affect Protein Function
inferredcites →https://doi.org/10.1517/14622416.3.1.131openalex-snapshot
Recent progress in multiple sequence alignment: a survey

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1093/nar/gki1020openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/nar/gkq443openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/nar/gkq501openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/nar/gkq982openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/nar/gkr220openalex-snapshot
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inferred← citeshttps://doi.org/10.1095/biolreprod.109.077438openalex-snapshot
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inferred← citeshttps://doi.org/10.1096/fj.11-190868openalex-snapshot
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inferred← citeshttps://doi.org/10.1104/pp.105.073510openalex-snapshot
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inferred← citeshttps://doi.org/10.1104/pp.107.111237openalex-snapshot
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inferred← citeshttps://doi.org/10.1104/pp.108.130450openalex-snapshot
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inferred← citeshttps://doi.org/10.1104/pp.108.132720openalex-snapshot
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inferred← citeshttps://doi.org/10.1104/pp.109.149625openalex-snapshot
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inferred← citeshttps://doi.org/10.1104/pp.112.203968openalex-snapshot
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inferred← citeshttps://doi.org/10.1105/tpc.107.051706openalex-snapshot
Common Functions for Diverse Small RNAs of Land Plants
inferred← citeshttps://doi.org/10.1105/tpc.113.112482openalex-snapshot
Trans-Golgi Network Localized ECHIDNA/Ypt Interacting Protein Complex Is Required for the Secretion of Cell Wall Polysaccharides inArabidopsis
inferred← citeshttps://doi.org/10.1110/ps.073277108openalex-snapshot
Enhancement of coenzyme binding by a single point mutation at the coenzyme binding domain of E. coli lactaldehyde dehydrogenase
inferred← citeshttps://doi.org/10.1111/1567-1364.12035openalex-snapshot
Heterologous expression ofCandida albicansPma1p inSaccharomyces cerevisiae
inferred← citeshttps://doi.org/10.1111/aos.12038openalex-snapshot
Novel OPA1 missense mutation in a family with optic atrophy and severe widespread neurological disorder
inferred← citeshttps://doi.org/10.1111/bph.12508openalex-snapshot
Receptor activity‐modifying protein‐dependent effects of mutations in the calcitonin receptor‐like receptor: implications for adrenomedullin and calcitonin gene‐related peptide pharmacology
inferred← citeshttps://doi.org/10.1111/j.1365-2958.2005.04848.xopenalex-snapshot
The solute‐binding component of a putative Mn(II) ABC transporter (MntA) is a novel Bacillus anthracis virulence determinant
inferred← citeshttps://doi.org/10.1111/j.1365-2958.2005.04902.xopenalex-snapshot
CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae
inferred← citeshttps://doi.org/10.1111/j.1365-2958.2008.06460.xopenalex-snapshot
Characterization of Bacillus anthracis iron‐regulated surface determinant (Isd) proteins containing NEAT domains
inferred← citeshttps://doi.org/10.1111/j.1365-2958.2010.07351.xopenalex-snapshot
Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing
inferred← citeshttps://doi.org/10.1111/j.1365-3040.2009.02035.xopenalex-snapshot
Small heat‐shock proteins and leaf cooling capacity account for the unusual heat tolerance of the central spike leaves inAgave tequilanavar. Weber
inferred← citeshttps://doi.org/10.1111/j.1365-3059.2009.02120.xopenalex-snapshot
The North American cranberry fruit rot fungal community: a systematic overview using morphological and phylogenetic affinities
inferred← citeshttps://doi.org/10.1111/j.1420-9101.2009.01901.xopenalex-snapshot
The evolution of South American endemic canids: a history of rapid diversification and morphological parallelism
inferred← citeshttps://doi.org/10.1111/j.1432-1033.2004.04245.xopenalex-snapshot
Structural and functional analysis of ataxin‐2 and ataxin‐3
inferred← citeshttps://doi.org/10.1111/j.1438-8677.2010.00362.xopenalex-snapshot
Physiology and biophysics of plant ligand‐gated ion channels
inferred← citeshttps://doi.org/10.1111/j.1438-8677.2011.00501.xopenalex-snapshot
Polygalacturonase‐inhibiting proteins – leucine‐rich repeat proteins in plant defence
inferred← citeshttps://doi.org/10.1111/j.1462-2920.2005.00843.xopenalex-snapshot
Putative novel photosynthetic reaction centre organizations in marine aerobic anoxygenic photosynthetic bacteria: insights from metagenomics and environmental genomics
inferred← citeshttps://doi.org/10.1111/j.1462-2920.2008.01657.xopenalex-snapshot
Phylogenetic analyses of ribosomal DNA‐containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre
inferred← citeshttps://doi.org/10.1111/j.1567-1364.2010.00629.xopenalex-snapshot
Ambiguous decoding of the CUG codon alters the functionality of the Candida albicans translation initiation factor 4E
inferred← citeshttps://doi.org/10.1111/j.1574-6941.2010.00968.xopenalex-snapshot
Combined eukaryotic and bacterial community fingerprinting of natural freshwater biofilms using automated ribosomal intergenic spacer analysis
inferred← citeshttps://doi.org/10.1111/j.1742-4658.2006.05285.xopenalex-snapshot
Characterization of the flavin association in hexose oxidase from Chondrus crispus
inferred← citeshttps://doi.org/10.1111/j.1742-4658.2012.08811.xopenalex-snapshot
Comparative structural and functional analysis of two octaheme nitrite reductases from closely related T hioalkalivibrio species
inferred← citeshttps://doi.org/10.1128/aem.00298-09openalex-snapshot
Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology
inferred← citeshttps://doi.org/10.1128/aem.01862-10openalex-snapshot
Identification and Characterization of Novel and Potent Transcription Promoters of Francisella tularensis
inferred← citeshttps://doi.org/10.1128/aem.02380-10openalex-snapshot
Recombination in Wolbachia Endosymbionts of Filarial Nematodes?
inferred← citeshttps://doi.org/10.1128/aem.71.3.1283-1290.2005openalex-snapshot
Novel Activator of Mannose-Specific Phosphotransferase System Permease Expression in Listeria innocua , Identified by Screening for Pediocin AcH Resistance
inferred← citeshttps://doi.org/10.1128/ec.00025-08openalex-snapshot
Identification of Mating Type Genes in the Bipolar Basidiomycetous Yeast Rhodosporidium toruloides : First Insight into the MAT Locus Structure of the Sporidiobolales
inferred← citeshttps://doi.org/10.1128/ec.00203-09openalex-snapshot
RNA Interference Silencing of a Major Lipid Droplet Protein Affects Lipid Droplet Size in Chlamydomonas reinhardtii
inferred← citeshttps://doi.org/10.1128/iai.01299-08openalex-snapshot
The Metal Homeostasis Protein, Lsp, of Streptococcus pyogenes Is Necessary for Acquisition of Zinc and Virulence
inferred← citeshttps://doi.org/10.1128/jb.00331-12openalex-snapshot
Ligand-Binding Properties and Conformational Dynamics of Autolysin Repeat Domains in Staphylococcal Cell Wall Recognition
inferred← citeshttps://doi.org/10.1128/jb.00432-10openalex-snapshot
Comparative Analysis of the Biochemical and Functional Properties of C-Terminal Domains of Autotransporters
inferred← citeshttps://doi.org/10.1128/jb.00451-06openalex-snapshot
A Novel Protein, TtpC, Is a Required Component of the TonB2 Complex for Specific Iron Transport in the Pathogens Vibrio anguillarum and Vibrio cholerae
inferred← citeshttps://doi.org/10.1128/jb.00755-07openalex-snapshot
The Hotdog Thioesterase EntH (YbdB) Plays a Role In Vivo in Optimal Enterobactin Biosynthesis by Interacting with the ArCP Domain of EntB
inferred← citeshttps://doi.org/10.1128/jb.01521-07openalex-snapshot
A Highly Conserved Protein of Unknown Function Is Required by Sinorhizobium meliloti for Symbiosis and Environmental Stress Protection
inferred← citeshttps://doi.org/10.1128/jvi.01170-08openalex-snapshot
Kaposi's Sarcoma-Associated Herpesvirus gH/gL: Glycoprotein Export and Interaction with Cellular Receptors
inferred← citeshttps://doi.org/10.1142/s0219720010004720openalex-snapshot
MALAKITE: AN AUTOMATIC TOOL FOR CHARACTERISATION OF STRUCTURE OF RELIABLE BLOCKS IN MULTIPLE ALIGNMENTS OF PROTEIN SEQUENCES
inferred← citeshttps://doi.org/10.1159/000104747openalex-snapshot
A System for the Random Mutagenesis of the Two-Peptide Lantibiotic Lacticin 3147: Analysis of Mutants Producing Reduced Antibacterial Activities
inferred← citeshttps://doi.org/10.1159/000317243openalex-snapshot
Characterization of Human Antigenic Proteins SchS21 and SchS34 from Stachybotrys chartarum
inferred← citeshttps://doi.org/10.11606/t.9.2017.tde-24042017-101741openalex-snapshot
Planejamento e síntese de tuberculostáticos potenciais com base na estrutura de maltosiltransferase (GlgE) de Mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1182/blood-2005-01-0010openalex-snapshot
Identification of a transiently exposed VE-cadherin epitope that allows for specific targeting of an antibody to the tumor neovasculature
inferred← citeshttps://doi.org/10.1186/1471-2105-10-219openalex-snapshot
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
inferred← citeshttps://doi.org/10.1186/1471-2105-11-222openalex-snapshot
Fine-tuning structural RNA alignments in the twilight zone
inferred← citeshttps://doi.org/10.1186/1471-2105-6-185openalex-snapshot
PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability
inferred← citeshttps://doi.org/10.1186/1471-213x-10-12openalex-snapshot
Sex and the single embryo: early deveopment in the Mediterranean fruit fly, Ceratitis capitata
inferred← citeshttps://doi.org/10.1186/1471-2148-13-153openalex-snapshot
Sequence analyses of the distal-less homeobox gene family in East African cichlid fishes reveal signatures of positive selection
inferred← citeshttps://doi.org/10.1186/1471-2148-7-106openalex-snapshot
Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure
inferred← citeshttps://doi.org/10.1186/1471-2148-7-97openalex-snapshot
The identity, distribution, and impacts of non-native apple snails in the continental United States
inferred← citeshttps://doi.org/10.1186/1471-2164-10-s1-s11openalex-snapshot
Genomic and systems evolution in Vibrionaceae species
inferred← citeshttps://doi.org/10.1186/1471-2229-11-79openalex-snapshot
In Medicago truncatula, water deficit modulates the transcript accumulation of components of small RNA pathways
inferred← citeshttps://doi.org/10.1186/1472-6793-9-8openalex-snapshot
Acclimatory responses of the Daphnia pulex proteome to environmental changes. II. Chronic exposure to different temperatures (10 and 20°C) mainly affects protein metabolism
inferred← citeshttps://doi.org/10.1186/1472-6793-9-9openalex-snapshot
Physiological responses of Daphnia pulex to acid stress
inferred← citeshttps://doi.org/10.1186/1472-6807-7-10openalex-snapshot
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1
inferred← citeshttps://doi.org/10.1186/1742-4682-10-56openalex-snapshot
Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5)
inferred← citeshttps://doi.org/10.1186/1756-0500-7-333openalex-snapshot
Sac Pox from the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius is a proficient lactonase
inferred← citeshttps://doi.org/10.1186/gb-2010-11-6-r60openalex-snapshot
Global fitness profiling of fission yeast deletion strains by barcode sequencing
inferred← citeshttps://doi.org/10.1186/s12866-022-02661-4openalex-snapshot
Pesticide residue exposure provides different responses of the microbiomes of distinct cultures of the stored product pest mite Acarus siro
inferred← citeshttps://doi.org/10.1194/jlr.r600028-jlr200openalex-snapshot
Molecular diversity and evolution of the large lipid transfer protein superfamily
inferred← citeshttps://doi.org/10.1242/jcs.03226openalex-snapshot
Microtubule nucleation: γ-tubulin and beyond
inferred← citeshttps://doi.org/10.1261/rna.7246805openalex-snapshot
Human mitochondrial TyrRS disobeys the tyrosine identity rules
inferred← citeshttps://doi.org/10.13028/rwy3-kh64openalex-snapshot
Roles of Cellular RNA-Dependent RNA Polymerases in Endogenous Small RNA Pathways in Caenorhabditis elegans: A Dissertation
inferred← citeshttps://doi.org/10.1371/annotation/a50e86c0-f779-4a4a-80e6-e634a11bbfa8openalex-snapshot
Correction: Impact of Genetic Background on Allele Selection in a Highly Mutable Candida albicans Gene, PNG2
inferred← citeshttps://doi.org/10.1371/journal.pgen.1000412openalex-snapshot
Multifactorial Regulation of a Hox Target Gene
inferred← citeshttps://doi.org/10.1371/journal.pgen.1002617openalex-snapshot
The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs
inferred← citeshttps://doi.org/10.1371/journal.pone.0001514openalex-snapshot
Homology Modeling of Dissimilatory APS Reductases (AprBA) of Sulfur-Oxidizing and Sulfate-Reducing Prokaryotes
inferred← citeshttps://doi.org/10.1371/journal.pone.0005130openalex-snapshot
Fascin-1 Promoter Activity Is Regulated by CREB and the Aryl Hydrocarbon Receptor in Human Carcinoma Cells
inferred← citeshttps://doi.org/10.1371/journal.pone.0007442openalex-snapshot
Structural and Functional Similarity between the Bacterial Type III Secretion System Needle Protein PrgI and the Eukaryotic Apoptosis Bcl-2 Proteins
inferred← citeshttps://doi.org/10.1371/journal.pone.0009614openalex-snapshot
Impact of Genetic Background on Allele Selection in a Highly Mutable Candida albicans Gene, PNG2
inferred← citeshttps://doi.org/10.1371/journal.pone.0010969openalex-snapshot
Species Used for Drug Testing Reveal Different Inhibition Susceptibility for 17beta-Hydroxysteroid Dehydrogenase Type 1
inferred← citeshttps://doi.org/10.1371/journal.pone.0012403openalex-snapshot
Mutational Characterization of the Bile Acid Receptor TGR5 in Primary Sclerosing Cholangitis
inferred← citeshttps://doi.org/10.1371/journal.pone.0017747openalex-snapshot
Interchromosomal Duplications on the Bactrocera oleae Y Chromosome Imply a Distinct Evolutionary Origin of the Sex Chromosomes Compared to Drosophila
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