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- Xrate abstract "XRATE is a program for prototyping phylogenetic hidden Markov models and stochastic context-free grammars. It is used to discover patterns of evolutionary conservation in sequence alignments. The program can be used to estimate parameters for such models from "training" alignment data, or to apply the parameterized model so as to annotate new alignments. The program allows specification of a variety of models of DNA sequence evolution which may be arbitrarily organized using formal grammars.As an example of how XRATE is used, consider a protein-coding gene consisting of exons interspersed with introns. The exons contain triplets of nucleotides (codons) that are translated by ribosomes according to the genetic code, and consequently are under selection pressure (since any mutation may affect the translated amino acid sequence). In contrast, the introns are under fewer selective constraints and tend to evolve faster. These varying pressures show up clearly in multiple alignments.The sequential layout of introns and exons can be described using grammar theory (from linguistics) and each of their distinct evolutionary signatures modeled as a continuous-time Markov process.XRATE allows the user to specify such models in a configuration file and estimate their parameters (evolutionary rates, length distributions of exons and introns, etc.) directly from alignment data, using the Expectation-maximization algorithm.XRATE can be downloaded as part of the DART software package. It accepts input files in Stockholm format.".
- Xrate developer University_of_California,_Berkeley.
- Xrate latestReleaseVersion "1".
- Xrate wikiPageExternalLink DART.
- Xrate wikiPageExternalLink XRATE.
- Xrate wikiPageExternalLink XrateFormat.
- Xrate wikiPageID "15302691".
- Xrate wikiPageLength "3067".
- Xrate wikiPageOutDegree "26".
- Xrate wikiPageRevisionID "678199017".
- Xrate wikiPageWikiLink Amino_acid_sequence.
- Xrate wikiPageWikiLink Apple_Macintosh.
- Xrate wikiPageWikiLink Category:Bioinformatics_software.
- Xrate wikiPageWikiLink Codons.
- Xrate wikiPageWikiLink Continuous-time_Markov_chain.
- Xrate wikiPageWikiLink Continuous-time_Markov_process.
- Xrate wikiPageWikiLink Cygwin.
- Xrate wikiPageWikiLink Evolutionary_pressure.
- Xrate wikiPageWikiLink Exon.
- Xrate wikiPageWikiLink Exons.
- Xrate wikiPageWikiLink Expectation-maximization_algorithm.
- Xrate wikiPageWikiLink Expectation–maximization_algorithm.
- Xrate wikiPageWikiLink Formal_grammar.
- Xrate wikiPageWikiLink Gene.
- Xrate wikiPageWikiLink Genetic_code.
- Xrate wikiPageWikiLink Hidden_Markov_model.
- Xrate wikiPageWikiLink Hidden_Markov_models.
- Xrate wikiPageWikiLink Intron.
- Xrate wikiPageWikiLink Introns.
- Xrate wikiPageWikiLink Linux.
- Xrate wikiPageWikiLink Macintosh.
- Xrate wikiPageWikiLink Models_of_DNA_evolution.
- Xrate wikiPageWikiLink Multiple_sequence_alignment.
- Xrate wikiPageWikiLink Peptide_sequence.
- Xrate wikiPageWikiLink Phylogenetic.
- Xrate wikiPageWikiLink Phylogenetics.
- Xrate wikiPageWikiLink Ribosome.
- Xrate wikiPageWikiLink Ribosomes.
- Xrate wikiPageWikiLink Selection_pressure.
- Xrate wikiPageWikiLink Sequence_alignment.
- Xrate wikiPageWikiLink Stochastic_context-free_grammar.
- Xrate wikiPageWikiLink Stockholm_format.
- Xrate wikiPageWikiLink UC_Berkeley.
- Xrate wikiPageWikiLink UNIX.
- Xrate wikiPageWikiLink University_of_California,_Berkeley.
- Xrate wikiPageWikiLink Unix.
- Xrate wikiPageWikiLink Windows_XP.
- Xrate wikiPageWikiLinkText "Xrate".
- Xrate developer "Ian Holmes".
- Xrate genre "Bioinformatics tool".
- Xrate hasPhotoCollection Xrate.
- Xrate latestReleaseVersion "1".
- Xrate licence "Open source".
- Xrate name "XRATE".
- Xrate operatingSystem "UNIX, Linux, Mac, Cygwin on Windows XP".
- Xrate website XRATE.
- Xrate wikiPageUsesTemplate Template:Infobox_Software.
- Xrate wikiPageUsesTemplate Template:Reflist.
- Xrate subject Category:Bioinformatics_software.
- Xrate hypernym Program.
- Xrate type Software.
- Xrate type Work.
- Xrate type CreativeWork.
- Xrate type Thing.
- Xrate type Q386724.
- Xrate type Q7397.
- Xrate comment "XRATE is a program for prototyping phylogenetic hidden Markov models and stochastic context-free grammars. It is used to discover patterns of evolutionary conservation in sequence alignments. The program can be used to estimate parameters for such models from "training" alignment data, or to apply the parameterized model so as to annotate new alignments.".
- Xrate label "Xrate".
- Xrate sameAs m.03m43rp.
- Xrate sameAs Q8045004.
- Xrate sameAs Q8045004.
- Xrate wasDerivedFrom Xrate?oldid=678199017.
- Xrate homepage XRATE.
- Xrate isPrimaryTopicOf Xrate.
- Xrate name "XRATE".