PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees

Whelan, Simon; Bakker, Paul I. W. de; Quévillon, Emmanuel; Rodríguez, Nicolás; Goldman, Nick

doi:10.1093/nar/gkj087

Cited by 62 publications

(56 citation statements)

References 36 publications

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“…We have calculated [11,12] the depth d for all trees (and subtrees) in the phylogenetic databases TreeBASE (containing species phylogenies [16]) and PANDIT (protein phylogenies [17]). The result in Figure 1(a) suggests that the average depth grows with the number of tips as…”

Section: Tree Shape and Depthmentioning

confidence: 99%

“…Based on genetic information, modern computational biology has inferred thousands of trees, socalled phylogenies [15], depicting the evolutionary relationships between sets of species, from bacteria to mammals [16]. The shapes of the collected phylogenies and of related evolutionary trees [17] share statistical properties not observed in trees generated by standard branching models [18][19][20]. It has been a long-standing and fundamental question in evolutionary biology to identify which processes accurately describe the observed tree shapes and thus may serve as models of biological evolution [21,22].…”

Section: Introductionmentioning

confidence: 99%

“…[16,17,24]), the ERM hypothesis can be rejected, as most real phylogenetic trees are significantly less balanced than those generated by the ERM and Yule models [11,21,22,24].…”

Section: Introductionmentioning

confidence: 99%

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Anomalous scaling in an age-dependent branching model

et al. 2015

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We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ −α . Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α = 1) tree depth grows as (log n)2 . This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.

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Section: Tree Shape and Depthmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Anomalous scaling in an age-dependent branching model

et al. 2015

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“…PANDITplus is a MySQL database built upon the PANDIT version 17.0, 2 Protein and Associated Nucleotide Domains with Inferred Trees derived from the seed alignments of Pfam-A. Each PANDIT entry includes amino acid and codon based alignments (with reliability estimates for each column) and estimates of phylogenetic trees inferred from these alignments.…”

Section: Structure Of Panditplusmentioning

confidence: 99%

PANDITplus: toward better integration of evolutionary view on molecular sequences with supplementary bioinformatics resources

Dimitrieva¹,

Anisimova

2010

Trends Evol Biol

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Recent comparative genomic and other large-scale bioinformatics studies increasingly have been using gene annotations, functional classifications, and complementary data from the emerging "-omics" disciplines. Indeed, such analyses have better chances to uncover hidden patterns in complex multidimensional and heterogeneous biological systems data. On the other hand, inferences from such studies are extremely sensitive to data samples and quality, and are more difficult to compare or replicate owing to differences in supplementary data sources at times not publicly available. As a contribution toward the unification and integration of good quality data from heterogeneous bioinformatics resources, we present here an integrated data bank PANDITplus. It is built as an extension of PANDIT, the database of PFAM alignments and phylogenetic trees for known protein domains and families spanning lineages from the three domains of life. PANDITplus is a relational database containing information on functional categories, metabolic pathways, protein-protein interactions, disease associations, gene expression, three-dimensional structure, as well as estimates from evolutionary analyses of selective pressures. User-friendly interface enables customized queries and fast data access. We recommend PANDITplus as a common bioinformatics platform for testing evolutionary hypotheses, which go beyond the mere inferences from molecular data by incorporating supplementary gene information. Equally, PANDITplus provides an excellent resource for the development, testing, and comparison of statistical models of substitution and probabilistic dependencies between a molecular sequence and its various attributes. The database may be accessed via http://www.panditplus.org.

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“…Furthermore, by using a substitution model centred about a fixed amino acid model, one can use prior information about amino acid substitution processes combined with the data at hand to produce valid phylogenetic inferences. Indeed, an alternative to producing fixed amino acid models is to produce distributions of substitution rates from databases of alignments, such as the Pandit database (Whelan et al 2003(Whelan et al , 2006.…”

Section: Drosophila Adh Vertebrate β-Globinmentioning

confidence: 99%

Bayesian analysis of amino acid substitution models

Huelsenbeck

Joyce

Lakner

et al. 2008

Phil. Trans. R. Soc. B

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Models of amino acid substitution present challenges beyond those often faced with the analysis of DNA sequences. The alignments of amino acid sequences are often small, whereas the number of parameters to be estimated is potentially large when compared with the number of free parameters for nucleotide substitution models. Most approaches to the analysis of amino acid alignments have focused on the use of fixed amino acid models in which all of the potentially free parameters are fixed to values estimated from a large number of sequences. Often, these fixed amino acid models are specific to a gene or taxonomic group (e.g. the Mtmam model, which has parameters that are specific to mammalian mitochondrial gene sequences). Although the fixed amino acid models succeed in reducing the number of free parameters to be estimated-indeed, they reduce the number of free parameters from approximately 200 to 0-it is possible that none of the currently available fixed amino acid models is appropriate for a specific alignment. Here, we present four approaches to the analysis of amino acid sequences. First, we explore the use of a general time reversible model of amino acid substitution using a Dirichlet prior probability distribution on the 190 exchangeability parameters. Second, we then explore the behaviour of prior probability distributions that are 'centred' on the rates specified by the fixed amino acid model. Third, we consider a mixture of fixed amino acid models. Finally, we consider constraints on the exchangeability parameters as partitions, similar to how nucleotide substitution models are specified, and place a Dirichlet process prior model on all the possible partitioning schemes.

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PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees

Cited by 62 publications

References 36 publications

Anomalous scaling in an age-dependent branching model

Anomalous scaling in an age-dependent branching model

PANDITplus: toward better integration of evolutionary view on molecular sequences with supplementary bioinformatics resources

Bayesian analysis of amino acid substitution models

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