Supplementary Data - Word file
... §S2.3. The Random Breakage Model of Genome Evolution As described in the main text, it has long been proposed that genomes evolve according to random breakage model which predicts that distances between breakpoints should follow an exponential distribution of the form f(x) = 1/L e-x/L, where L is t ...
... §S2.3. The Random Breakage Model of Genome Evolution As described in the main text, it has long been proposed that genomes evolve according to random breakage model which predicts that distances between breakpoints should follow an exponential distribution of the form f(x) = 1/L e-x/L, where L is t ...
A Plastid in the Making: Evidence for a Second
... abbreviations, see Methods) and EMBL/GENBANK accession numbers are given. Sequences determined new to this study are in bold. Encircled numbers (1—7) denote clades analyzed by single gene- and partitioned analyses (see Results and Discussion, and Table 1). The inset shows a light micrograph of a cel ...
... abbreviations, see Methods) and EMBL/GENBANK accession numbers are given. Sequences determined new to this study are in bold. Encircled numbers (1—7) denote clades analyzed by single gene- and partitioned analyses (see Results and Discussion, and Table 1). The inset shows a light micrograph of a cel ...
Time Dependency of Molecular Rate Estimates and Systematic
... to them together as the ‘‘rate of change.’’ To investigate the transition between the short-term mutation rate and long-term substitution rate, we estimate rates of change from mitochondrial sequences of avian and primate taxa and compare these rates in the context of the timescales on which they we ...
... to them together as the ‘‘rate of change.’’ To investigate the transition between the short-term mutation rate and long-term substitution rate, we estimate rates of change from mitochondrial sequences of avian and primate taxa and compare these rates in the context of the timescales on which they we ...
IOSR Journal of Computer Engineering (IOSR-JCE)
... For each point, compute its coefficients of being in the clusters, using the formula above. Although algorithm minimizes intra-cluster variance as well, it has the same problems as in k-means where the results depend on the initial choice of weights. Self-Organizing-Map Clustering Self-organizing-ma ...
... For each point, compute its coefficients of being in the clusters, using the formula above. Although algorithm minimizes intra-cluster variance as well, it has the same problems as in k-means where the results depend on the initial choice of weights. Self-Organizing-Map Clustering Self-organizing-ma ...
Abstract Citrus is the main fruit crop in the world and Spain is the 6th
... genotyping methods offers the possibility to utilize a broad range of molecular markers in genotyping triploid genotypes. Both methods have been used in further works included in this thesis. SDR has been demonstrated as the mechanism underlying unreduced gamete production in ‘Fortune’ mandarin by ...
... genotyping methods offers the possibility to utilize a broad range of molecular markers in genotyping triploid genotypes. Both methods have been used in further works included in this thesis. SDR has been demonstrated as the mechanism underlying unreduced gamete production in ‘Fortune’ mandarin by ...
2.4. Sequence databases
... relational databases e.g. it is not so easy to add additional data to the database, therefore the whole database structure needs to be updated. There is also a risk that some of the relationships between objects may be misrepresented. Some current databases have therefore incorporated features of bo ...
... relational databases e.g. it is not so easy to add additional data to the database, therefore the whole database structure needs to be updated. There is also a risk that some of the relationships between objects may be misrepresented. Some current databases have therefore incorporated features of bo ...
Mgr. Martina Višňovská Alignments on Sequences with Internal
... we multiply this size by four to account for the fact that in a uniformly random database, we need two bits to encode each nucleotide. In this way, we obtain an estimate of the effective database size which can be used in any formula or algorithm for estimating P -values on uniformly distributed data ...
... we multiply this size by four to account for the fact that in a uniformly random database, we need two bits to encode each nucleotide. In this way, we obtain an estimate of the effective database size which can be used in any formula or algorithm for estimating P -values on uniformly distributed data ...
Kernel Approaches for Nonlinear Genetic Association Regression
... The genetic information collected in genome-wide association studies (GWAS) is represented by the genotypes of various single-nucleotid polymorphisms (SNPS). Testing biological meaningful SNP Sets is a successful strategy for the evaluation of GWAS data, as it may increase power as well as interpret ...
... The genetic information collected in genome-wide association studies (GWAS) is represented by the genotypes of various single-nucleotid polymorphisms (SNPS). Testing biological meaningful SNP Sets is a successful strategy for the evaluation of GWAS data, as it may increase power as well as interpret ...
Comprehensive Exam Mainul Islam Department of Computer
... and improve the quality of analysis results. • For example, during regression testing, differences can be used to focus re-testing efforts by selecting only test cases that exercise the modified code. ...
... and improve the quality of analysis results. • For example, during regression testing, differences can be used to focus re-testing efforts by selecting only test cases that exercise the modified code. ...
LDhat 2.2: A package for the population genetic analysis of
... option allows efficient analysis of small data sets. However, other options within the program (such as conditional simulation - see below) require the exhaustive lookup file generated by complete or lkgen. The program also performs additional analyses of recombination including estimation of the mi ...
... option allows efficient analysis of small data sets. However, other options within the program (such as conditional simulation - see below) require the exhaustive lookup file generated by complete or lkgen. The program also performs additional analyses of recombination including estimation of the mi ...
Microarray Data Analysis Using BASE - MGH-PGA
... – How do I find interesting stuff? – learn some analysis tools – How do I trust the results? – statistics is key ...
... – How do I find interesting stuff? – learn some analysis tools – How do I trust the results? – statistics is key ...
Introduction slides on BASE
... – How do I find interesting stuff? – learn some analysis tools – How do I trust the results? – statistics is key ...
... – How do I find interesting stuff? – learn some analysis tools – How do I trust the results? – statistics is key ...
Molecualr Biology and Evolution
... made, but the NifD phylogeny lacked resolution. Here nifgene phylogeny is addressed with a phylogenetic analysis of a third and longer nifgene, nzyK. As part of the study, the nifK gene of the key taxon Frankia was sequenced. Parsimony and some distance analyses of the nifK amino acid sequences prov ...
... made, but the NifD phylogeny lacked resolution. Here nifgene phylogeny is addressed with a phylogenetic analysis of a third and longer nifgene, nzyK. As part of the study, the nifK gene of the key taxon Frankia was sequenced. Parsimony and some distance analyses of the nifK amino acid sequences prov ...
Package `FAMT`
... The method proposed in this package takes into account the impact of dependence on multiple testing procedures for high-throughput data as proposed by Friguet et al. (2009). The common information shared by all the variables is modeled by a factor analysis structure. The number of factors considered ...
... The method proposed in this package takes into account the impact of dependence on multiple testing procedures for high-throughput data as proposed by Friguet et al. (2009). The common information shared by all the variables is modeled by a factor analysis structure. The number of factors considered ...
Random survival forests for highdimensional data
... grown to full size and then pruned back on the basis of a complexity measure. However, RF trees differ from classical CART as they are grown nondeterministically, without pruning, using a two-stage randomization procedure. First, an independent bootstrap sample of the data is drawn over which the tr ...
... grown to full size and then pruned back on the basis of a complexity measure. However, RF trees differ from classical CART as they are grown nondeterministically, without pruning, using a two-stage randomization procedure. First, an independent bootstrap sample of the data is drawn over which the tr ...
09ConsensusGene
... Greedy consensus trees are constructed by sequentially is the only 2-taxon clade which satisfies rule 2 and no adding one clade at a time, the most frequently occurr- 3-taxon clade satisfies rule 3. For these input trees, the ing clade that is compatible with clades already included majority-rule co ...
... Greedy consensus trees are constructed by sequentially is the only 2-taxon clade which satisfies rule 2 and no adding one clade at a time, the most frequently occurr- 3-taxon clade satisfies rule 3. For these input trees, the ing clade that is compatible with clades already included majority-rule co ...
Quantitative analysis of electrophoresis data: novel curve fitting
... electrophoresis results have suffered from a variety of limitations As a result, no standard for high-resolution, quantitative analysi of electrophoretograms has been adopted. In order to realize th( full potential of the electrophoresis technique, an easy, reliabl( method for quantitative analysis ...
... electrophoresis results have suffered from a variety of limitations As a result, no standard for high-resolution, quantitative analysi of electrophoretograms has been adopted. In order to realize th( full potential of the electrophoresis technique, an easy, reliabl( method for quantitative analysis ...
Concordance trees, concordance factors, and the exploration of
... that involve reticulation at the population level (e.g., introgression, lateral gene transfer). Instead of estimating a population history from the molecular data it seems possible that one might be able to use the sample of gene genealogies represented in a dataset to directly estimate the proporti ...
... that involve reticulation at the population level (e.g., introgression, lateral gene transfer). Instead of estimating a population history from the molecular data it seems possible that one might be able to use the sample of gene genealogies represented in a dataset to directly estimate the proporti ...
Analysis of multiple phenotypes in genome
... In multivariate regression, the response variables are assumed to follow some specific multivariate distribution, most commonly a multi-normal distribution, although this is a strong and sometimes unwarranted assumption. Principal component analysis ...
... In multivariate regression, the response variables are assumed to follow some specific multivariate distribution, most commonly a multi-normal distribution, although this is a strong and sometimes unwarranted assumption. Principal component analysis ...
Analysis of multiple phenotypes in genome-wide genetic mapping studies Open Access
... In multivariate regression, the response variables are assumed to follow some specific multivariate distribution, most commonly a multi-normal distribution, although this is a strong and sometimes unwarranted assumption. Principal component analysis ...
... In multivariate regression, the response variables are assumed to follow some specific multivariate distribution, most commonly a multi-normal distribution, although this is a strong and sometimes unwarranted assumption. Principal component analysis ...
An R Package for belief propagation in genotype
... Hugin domains. The domains that are not saved will be lost when quitting R. The use of assignment operator such as <- or = will only return the pointer. Refer to the RHugin help manual for more information. The other elements in the list are for internal use with other functions. ...
... Hugin domains. The domains that are not saved will be lost when quitting R. The use of assignment operator such as <- or = will only return the pointer. Refer to the RHugin help manual for more information. The other elements in the list are for internal use with other functions. ...
Genomic scans for selective sweeps using SNP data
... aberrant frequency spectra. However, in principle, power could be gained by considering the fashion in which a selective sweep changes the frequency spectrum. In the following, we describe a method for detecting selective sweeps that is based on considerations of the way the spatial distribution (al ...
... aberrant frequency spectra. However, in principle, power could be gained by considering the fashion in which a selective sweep changes the frequency spectrum. In the following, we describe a method for detecting selective sweeps that is based on considerations of the way the spatial distribution (al ...
Yang (2002) - molecularevolution.org
... example is presented later in this section.) This approach may suffer from several problems. First, reconstructed ancestral sequences are not real data and involve systematic biases and random errors [19]. Second, the methods used to estimate substitution rates along each branch are typically simpli ...
... example is presented later in this section.) This approach may suffer from several problems. First, reconstructed ancestral sequences are not real data and involve systematic biases and random errors [19]. Second, the methods used to estimate substitution rates along each branch are typically simpli ...
Y-Chromosome Marker S28 / U152 Haplogroup
... ”Of interest is the fact that while R-U152 has a clear French-Italian center of weight, the locations exhibiting highest STR variance are Germany and Slovakia, i.e., Central Europe. My guess is that R-U152 originated in Central Europe spreading to the west and south, perhaps with Italo-Celtic speak ...
... ”Of interest is the fact that while R-U152 has a clear French-Italian center of weight, the locations exhibiting highest STR variance are Germany and Slovakia, i.e., Central Europe. My guess is that R-U152 originated in Central Europe spreading to the west and south, perhaps with Italo-Celtic speak ...
NOCARDIA sp. INDONESIAN VOLCANIC SOIL DESAK GEDE SRI ANDAYANI , ELIN YULINAH SUKANDAR
... using Clustal X and NJ plot program. To construct the phylogenetic trees, the homology sequence from BLAST and FASTA format results was calculated the data for three construction by Clustal X, and then conversion of calculated data into trees by NJ plot. Neighbors-joining (NJ) method is the simple p ...
... using Clustal X and NJ plot program. To construct the phylogenetic trees, the homology sequence from BLAST and FASTA format results was calculated the data for three construction by Clustal X, and then conversion of calculated data into trees by NJ plot. Neighbors-joining (NJ) method is the simple p ...