APDB: a novel measure for benchmarking sequence alignment methods without reference alignments

No abstract is available for this paper.

• Publication year

  2003

• Venue

  Intelligent Systems in Molecular Biology

• Publication date

  2003-07-03

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btg1029PMID 12855461
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Alignment

  2009influential reference
• Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set

  2001cited by this paper
• A study of quality measures for protein threading models

  2001cited by this paper
• Multiple alignments for structural functional or phylogenetic analyses of homologous sequences

  2000cited by this paper
• ProSup: a refined tool for protein structure alignment.

  2000cited by this paper
• MaxSub: an automated measure for the assessment of protein structure prediction quality

  2000cited by this paper
• T-Coffee: A novel method for fast and accurate multiple sequence alignment.

  2000influential reference
• HOMSTRAD: A database of protein structure alignments for homologous families

  1998cited by this paper
• SAGA: sequence alignment by genetic algorithm.

  1996influential reference
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

  1994influential reference
• A data bank merging related protein structures and sequences.

  1992cited by this paper
• A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons.

  1987cited by this paper

• eCOMPASS: evaluative comparison of multiple protein alignments by statistical score

  2021cites this paper
• Mutations in coral soma and sperm imply lifelong stem cell renewal and cell lineage selection

  2021cites this paper
• Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation

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• Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis

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• A chromosome-level genome assembly and annotation of the humpback grouper Cromileptes altivelas

  2020cites this paper
• High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)

  2020cites this paper
• Genome-wide local ancestries discriminate homoploid hybrid speciation from secondary introgression in the red wolf (Canidae: Canis rufus)

  2020cites this paper
• Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)

  2020cites this paper
• Chromosome-level genome assembly of a regenerable maize inbred line A188

  2020cites this paper
• Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains

  2020cites this paper
• The Contributions of the Allopolyploid Parents of the Mesopolyploid Brassiceae are Evolutionarily Distinct but Functionally Compatible

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• A bird’s white-eye view on neosex chromosome evolution

  2019cites this paper
• Genetic basis of species-specific genitalia reveals role in species diversification

  2019cites this paper
• The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants

  2019cites this paper
• Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga

  2018cites this paper
• The tempo of linked selection: rapid emergence of a heterogeneous genomic landscape during a radiation of monkeyflowers

  2018cites this paper
• Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus

  2018cites this paper
• Massive gene amplification on a recently formed Drosophila Y-chromosome

  2018cites this paper
• De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

  2017cites this paper
• Architecture and Distribution of Introns in Core Genes of Four Fusarium Species

  2017cites this paper
• Multiple sequence alignment modeling: methods and applications

  2016cites this paper
• An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

  2016cites this paper
• The Genome and Methylome of a Subsocial Small Carpenter Bee, Ceratina calcarata

  2016cites this paper
• A Meiotic Drive Element in the Maize Pathogen Fusarium verticillioides Is Located Within a 102 kb Region of Chromosome V

  2016cites this paper
• Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix

  2015cites this paper
• Dynamical and Topological Tools for (Modern) Music Analysis. (Outils dynamiques et topologiques pour l'analyse musicale)

  2015cites this paper
• IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments

  2015cites this paper
• T-Coffee: Tree-based consistency objective function for alignment evaluation.

  2014cites this paper
• Draft Sequences of the Radish (Raphanus sativus L.) Genome

  2014cites this paper
• Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

  2014cites this paper
• Workflow for Building a Draft Genome Assembly using Public-domain Tools: Toxocara canis as a Case Study

  2014cites this paper
• FAQMAA : A Framework for Automatic Quality Assessment of Multiple Sequence Alignments

  2013cites this paper
• MQAT: An Efficient Quality Assessment Tool for Large Multiple Sequence Alignments

  2013cites this paper
• The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes

  2013cites this paper
• Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude

  2013cites this paper
• Tools to kill: Genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina

  2012cites this paper
• Improving the Alignment Quality of Consistency Based Aligners with an Evaluation Function Using Synonymous Protein Words

  2011cites this paper
• Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

  2011cites this paper
• CLUSTAL W Analysis of Cytochrome b Based Genetic Diversity of Osteichthyes

  2011cites this paper
• Gene Duplication and Environmental Adaptation within Yeast Populations

  2010cites this paper
• T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors.

  2010cites this paper
• Quality measures for protein alignment benchmarks

  2010cites this paper
• Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach

  2009cites this paper
• 25 Protein Multiple Sequence Alignment

  2009cites this paper
• Sequence Analysis Upcoming Challenges for Multiple Sequence Alignment Methods in the High-Throughput Era

  2009cites this paper
• Sequence Conservation Metrics: Implementation and Comparative Analysis Master’s Thesis

  2009cites this paper
• Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.

  2008cites this paper
• TURUN YLIOPISTON JULKAISUJA

  2008cites this paper
• Protein multiple sequence alignment.

  2008cites this paper
• Using structural information in modeling and multiple alignments for phylogenetics.

  2008cites this paper
• Statistical Methods for Conservation and Alignment Quality in Proteins

  2008cites this paper
• Functional Proteomics

  2008cites this paper
• Prediction of cancer driver mutations in protein kinases.

  2008cites this paper
• New Methods for the Prediction and Classification of Protein Domains

  2007cites this paper
• Recent Evolutions of Multiple Sequence Alignment Algorithms

  2007cites this paper
• A statistical score for assessing the quality of multiple sequence alignments

  2006cites this paper
• MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information

  2006cites this paper
• APDB: a web server to evaluate the accuracy of sequence alignments using structural information

  2006cites this paper
• The iRMSD: a local measure of sequence alignment accuracy using structural information

  2006cites this paper
• RNA-Alignments und RNA-Struktur in silico

  2006cites this paper
• Multiple sequence alignments.

  2005cites this paper
• A word-oriented approach to alignment validation

  2005cites this paper
• Genomics of the fungal kingdom: insights into eukaryotic biology.

  2005cites this paper
• From Sequence to Structure And Back Again: An Alignment Tale

  2005cites this paper
• Protein homology detection by HMM?CHMM comparison

  2005cites this paper
• Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions.

  2005cites this paper
• Automatic assessment of alignment quality

  2005cites this paper
• QUASAR - scoring and ranking of sequence-structure alignments

  2005cites this paper
• Genome annotation past, present, and future: how to define an ORF at each locus.

  2005cites this paper
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.

  2004cites this paper
• 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment

  2004cites this paper