A new generation of homology search tools based on probabilistic inference.

Keywords

Probabilistic logic, Inference, Computer science, Hidden Markov model, Statistical model

References

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• A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance EstimationSean R. Eddy — 2008
• Basic local alignment search tool.Stephen F. Altschul, Warren Gish, Webb Miller — 1990
• A reliable sequence alignment method based on probabilities of residue correspondences.Sanzo Miyazawa — 1995
• Identification of common molecular subsequences.Temple F. Smith, Michael S. Waterman — 1981
• Rapid Significance Estimation in Local Sequence Alignment with GapsRalf Bundschuh — 2001
• Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.Samuel Karlin, Stephen F. Altschul — 1990
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• Hybrid alignment: high-performance with universal statisticsYi‐Kuo Yu, Ralf Bundschuh, Terence Hwa — 2002
• The estimation of statistical parameters for local alignment score distributions.Stephen F. Altschul — 2001
• Hidden Markov models for detecting remote protein homologiesKevin Karplus, Curtis L. Barrett, Richard Hughey — 1998
• Calibrating E-values for hidden Markov models using reverse-sequence null modelsKevin Karplus, Rachel Karchin, George Shackelford — 2005
• Rapid Assessment of Extremal Statistics for Gapped Local AlignmentRolf Erik Olsen, Ralf Bundschuh, Terence Hwa — 1999
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Stephen F. Altschul — 1997
• On the Problem of the Most Efficient Tests of Statistical HypothesesJerzy Neyman, Egon S. Pearson — 1933
• The Pfam protein families databaseROBERT FINN, Jaina Mistry, John Tate — 2007
• Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic AcidsRichard Durbin, Sean Eddy, Anders Krogh — 1998
• Studies in Probabilistic Sequence Alignment and EvolutionIan Holmes, Ewan Birney, Bill Bruno — 1998

Cited by

• Emergent complexity in Myosin V-based organelle inheritance.A. Blancas, Gloria Maribel Trejo Aguilar, Carlos Huitrón — 2012
• Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.Vicente María Escuin y Palop — 2012
• De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervisJoanne B. Mulcahy — 2014
• A Key Regulator of the Glycolytic and Gluconeogenic Central Metabolic Pathways in Sinorhizobium melilotiCatherine Benezech — 2017
• The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinnaZigor de la Quintana Ibáñez — 2018
• Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza淳一 藤田 — 2018
• Genetic repertoires of anaerobic microbiomes driving generation of biogasSantiago Muñoz Machado, Juan Lucio — 2018
• ARGDIT: a validation and integration toolkit for Antimicrobial Resistance Gene Databases和雄 中林 — 2018
• Acceleration of a bioinformatics application using high-level synthesis. (Accélération d'une application en bioinformatique utilisant une synthèse de haut niveau)Naeem Abbas, DERRIEN, Steven, QUINTON, Patrice — 2012
• Microbial Friends And Foes: Characterizing The Cnidarian Response To Pathogenic And Mutualistic MicroorganismsMorgan E. Mouchka — 2014
• Computational approaches to the study of human trypanosomatid infectionsJ. Weirather — 2012
• The relationship between orthology, protein domain architecture and protein functionSofia K. Forslund — 2011
• Methods for High-Throughput Comparative genomics and Distributed sequence AnalysisSamuel V. Angiuoli — 2011
• Deducing intracellular distributions of metabolic pathways from genomic data.Ansgar Gruber, Peter G. Kroth — 2014
• The Membrane Proteome : Evolution, Characteristics and ClassificationMarkus Sällman Almén — 2012
• Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: a case study of pIncA/C plasmids.Pablo Vinuesa, Bruno Contreras‐Moreira — 2015
• A Graphical and Numerical Approach for Functional Annotation and Phylogenetic InferenceGuillermı́n Agüero-Chapin — 2013
• Promotion of Bone Morphogenetic Protein Signaling by Tetraspanins and GlycosphingolipidsZhiyu Liu, Herong Shi, Lindsey C. Szymczak — 2015
• Models and Algorithms for Genome EvolutionCédric Chauve, Nadia El-Mabrouk, Éric Tannier — 2013
• Analyses of functional sequence in mammalian and avian genomesChris M Rands — 2014

Related papers

• Fast gapped-read alignment with Bowtie 2Ben Langmead, Steven L. Salzberg — 2012
• MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and UsabilityKazutaka Katoh, Daron M. Standley — 2013
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Stephen F. Altschul — 1997
• Pfam: the protein families databaseROBERT FINN, Alex Bateman, Jody Clements — 2013
• The Pfam protein families databaseAlex Bateman — 2011
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.R. C. Edgar — 2004
• Basic local alignment search tool.Stephen F. Altschul, Warren Gish, Webb Miller — 1990
• Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequencesWeizhong Li, Adam Godzik — 2006
• FastTree 2 – Approximately Maximum-Likelihood Trees for Large AlignmentsMorgan N. Price, Paramvir Dehal, Adam P. Arkin — 2010