RESUMO
UNLABELLED: Clann has been developed in order to provide methods of investigating phylogenetic information through the application of supertrees. AVAILABILITY: Clann has been precompiled for Linux, Apple Macintosh and Windows operating systems and is available from http://bioinf.may.ie/software/clann. Source code is available on request from the authors. SUPPLEMENTARY INFORMATION: Clann has been written in the C programming language. Source code is available on request.
Assuntos
Algoritmos , Evolução Biológica , Modelos Genéticos , Linhagem , Software , Análise por Conglomerados , Simulação por ComputadorRESUMO
MOTIVATION: In recent years there has been increased interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large number of taxa, it is not feasible to construct large and accurate trees using only a single processor. A number of specialized parallel programs have been produced in an attempt to address the huge computational requirements of maximum likelihood. We express a number of concerns about the current set of parallel phylogenetic programs which are currently severely limiting the widespread availability and use of parallel computing in maximum likelihood-based phylogenetic analysis. RESULTS: We have identified the suitability of phylogenetic analysis to large-scale heterogeneous distributed computing. We have completed a distributed and fully cross-platform phylogenetic tree building program called distributed phylogeny reconstruction by maximum likelihood. It uses an already proven maximum likelihood-based tree building algorithm and a popular phylogenetic analysis library for all its likelihood calculations. It offers one of the most extensive sets of DNA substitution models currently available. We are the first, to our knowledge, to report the completion of a distributed phylogenetic tree building program that can achieve near-linear speedup while only using the idle clock cycles of machines. For those in an academic or corporate environment with hundreds of idle desktop machines, we have shown how distributed computing can deliver a 'free' ML supercomputer.
Assuntos
Algoritmos , Evolução Molecular , Modelos Genéticos , Filogenia , Alinhamento de Sequência/métodos , Análise de Sequência de DNA/métodos , Simulação por Computador , Funções Verossimilhança , Modelos Estatísticos , SoftwareRESUMO
A software program CRANN has been developed in order to detect adaptive evolution in protein-coding DNA sequences.
Assuntos
Sequência de Bases/genética , Evolução Molecular , Software , Fases de Leitura Aberta/genética , FilogeniaRESUMO
With more than 10 fully sequenced, publicly available prokaryotic genomes, it is now becoming possible to gain useful insights into genome evolution. Before the genome era, many evolutionary processes were evaluated from limited data sets and evolutionary models were constructed on the basis of small amounts of evidence. In this paper, I show that genes on the Borrelia burgdorferi genome have two separate, distinct, and significantly different codon usages, depending on whether the gene is transcribed on the leading or lagging strand of replication. Asymmetrical replication is the major source of codon usage variation. Replicational selection is responsible for the higher number of genes on the leading strands, and transcriptional selection appears to be responsible for the enrichment of highly expressed genes on these strands. Replicational-transcriptional selection, therefore, has an influence on the codon usage of a gene. This is a new paradigm of codon selection in prokaryotes.
Assuntos
Grupo Borrelia Burgdorferi/genética , Códon , Replicação do DNA , Transcrição Gênica , Genoma BacterianoRESUMO
UNLABELLED: The program General Codon Usage Analysis (GCUA) has been developed for analysing codon and amino acid usage patterns. AVAILABILITY: ftp://ftp.nhm.ac.uk/pub/gcua. Freely available for academic use, commercial users should contact the author. CONTACT: J.McInerney@nhm.ac.uk
Assuntos
Sequência de Aminoácidos , Códon , Sistemas de Gerenciamento de Base de Dados , Análise MultivariadaRESUMO
The 16S ribosomal RNA gene from the beer-spoilage organism, Megasphaera cerevisiae was polymerase chain reaction (PCR)-amplified and sequenced. Analysis confirmed the phylogenetic position of M. cerevisiae as a sister taxon of Megasphaera elsdenii, within the obligately anaerobic, Gram-negative cocci. The sequence obtained should facilitate the development of DNA probes for early detection of this spoilage organism.
Assuntos
Cerveja/microbiologia , Cocos Anaeróbios Gram-Negativos/genética , RNA Bacteriano/genética , RNA Ribossômico 16S/genética , Sequência de Bases , Dados de Sequência Molecular , Filogenia , Reação em Cadeia da Polimerase , Alinhamento de SequênciaRESUMO
Studies on mammalian alpha-1-microglobulin/bikunin (AMBP) protein sequences suggest the ancestral AMBP gene arose between 270 and 80 million years ago. Here we report a similar study including recently reported piscine AMBP messenger RNA sequences. The analysis implies a far earlier data for the assembly of the ancestral AMBP gene, more than 450 million years ago. Similarly, a revised date for the origin of the ancestral Kunitz-type protein is estimated at approximately 875 million years ago. Evolutionary conservation is apparent among all the AMBP amino acid sequences. This implies a common functional significance in both teleosts and mammals. However, an unusually rapid rate of evolution is observed for domain II of the piscine bikunin sequences, suggesting that this domain is no longer truly orthologous in fish.
Assuntos
alfa-Globulinas/genética , Peixes/genética , Glicoproteínas/genética , Glicoproteínas de Membrana , Inibidores de Proteases/classificação , Inibidor da Tripsina de Soja de Kunitz , Sequência de Aminoácidos , Animais , Dados de Sequência Molecular , Filogenia , RNA Mensageiro/genética , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade da EspécieAssuntos
Archaea/isolamento & purificação , Bactérias/isolamento & purificação , Meio Ambiente , Microbiologia da Água , Archaea/classificação , Archaea/genética , Bactérias/classificação , Bactérias/genética , Sequência de Bases , Sequência Conservada , DNA Bacteriano , DNA Ribossômico/genética , Células Eucarióticas , Filogenia , Reação em Cadeia da Polimerase , Água do MarRESUMO
In 1992, two independent reports based on small-subunit rRNA gene (SSU rDNA) cloning revealed the presence of novel Archaea among marine bacterioplankton. Here, we report the presence of further novel Archaea SSU rDNA sequences recovered from the midgut contents of a deep-sea marine holothurian. Phylogenetic analyses show that these abyssal Archaea are a paraphyletic component of a highly divergent clade that also includes some planktonic sequences. Our data confirm that this clade is a deep-branching lineage in the tree of life.
