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BioJava: an open-source framework for bioinformatics in 2012
- Page 10 of 11 Original article Database, Vol. 2013, Article ID bat051, doi:10.1093/database/bat051 ............................................................................................................................................................
, 2012
"... Motivation: BioJava is an open-source project for processing of bio-logical data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality. Results: BioJava now consists of several independent mo ..."
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Motivation: BioJava is an open-source project for processing of bio-logical data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality. Results: BioJava now consists of several independent modules that provide state of the art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modications, and prediction of disordered regions in proteins, as well as parsers for common le formats using a biologically meaningful data model. Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website
TIGRFAMs and genome properties in 2013
- Nucleic Acids Res
, 2013
"... TIGRFAMs, available online at ..."
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ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res
, 2012
"... Bacteria ..."
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An improved predictive recognition model for Cys(2)- His(2) zinc finger proteins
- Nucleic Acids Res
, 2014
"... Cys2-His2 zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the s ..."
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Cys2-His2 zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred by homology due to the diversity of recognition residues present within individual fingers. Given the large number of unique zinc fingers and assemblies present across eukary-otes, a comprehensive predictive recognition model that could accurately estimate the DNA-binding specificity of any ZFP based on its amino acid sequence would have great utility. Toward this goal, we have used the DNA-binding specificities of 678 two-finger modules from both natural and artificial sources to construct a random forest-based predictive model for ZFP recognition. We find that our recognition model outperforms previ-ously described determinant-based recognition models for ZFPs, and can successfully estimate the specificity of naturally occurring ZFPs with previously defined specificities.
JPred4: a protein secondary structure prediction server
- Nucleic Acids Res
, 2015
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SecReT4: a web-based bacterial type IV secretion system resource
, 2012
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Large-scale multiple sequence alignment and phylogeny estimation
, 2013
"... With the advent of next generation sequencing technologies, alignment and phylogeny estimation of datasets with thousands of sequences is being attempted. To address these challenges, new algorithmic approaches have been developed that have been able to provide substantial improvements over standard ..."
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Cited by 5 (0 self)
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With the advent of next generation sequencing technologies, alignment and phylogeny estimation of datasets with thousands of sequences is being attempted. To address these challenges, new algorithmic approaches have been developed that have been able to provide substantial improvements over standard methods. This paper focuses on new approaches for ultra-large tree estimation, including methods for co-estimation of alignments and trees, estimating trees without needing a full sequence alignment, and phylogenetic placement. While the main focus is on methods with empirical performance advantages, we also discuss the theoretical guarantees of methods under Markov models of evolution. Finally, we include a discussion of the future of large-scale phylogenetic analysis.
Self-Deception and the Nature of
- Mind”, in McLaughlin and Rorty
, 1988
"... platform (GNP) for the discovery of modular ..."
A rticle Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution
"... Phylostratigraphy is a method for dating the evolutionary emergence of a gene or gene family by identifying its homologs across the tree of life, typically by using BLAST searches. Applying this method to all genes in a species, or genomic phylostratigraphy, allows investigation of genome-wide patte ..."
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Phylostratigraphy is a method for dating the evolutionary emergence of a gene or gene family by identifying its homologs across the tree of life, typically by using BLAST searches. Applying this method to all genes in a species, or genomic phylostratigraphy, allows investigation of genome-wide patterns in new gene origination at different evolutionary times and thus has been extensively used. However, gene age estimation depends on the challenging task of detecting distant homologs via sequence similarity, which is expected to have differential accuracies for different genes. Here, we evaluate the accuracy of phylostratigraphy by realistic computer simulation with parameters estimated from genomic data, and investigate the impact of its error on findings of genome evolution. We show that 1) phylostratigraphy substantially underestimates gene age for a considerable fraction of genes, 2) the error is especially serious when the protein evolves rapidly, is short, and/or its most conserved block of sites is small, and 3) these errors create spurious nonuniform distributions of various gene properties among age groups, many of which cannot be predicted a priori. Given the high likelihood that conclusions about gene age are faulty, we advocate the use of realistic simulation to determine if observations from phylostratigraphy are explainable, at least qualitatively, by a null model of biasedmeasurement, and in all cases, critical evaluation of results. Key words: BLAST, gene age, phylogenetic dating.
Paar-repeat proteins sharpen and diversify the type vi secretion system spike. Nature 2013, 500, 350–353. [CrossRef] [PubMed
"... These authors contributed equally to this work. The bacterial type VI secretion system (T6SS) is a large multi-component, dynamic macromolecular machine that plays an important role in the ecology of many Gram negative bacteria. T6SS is responsible for translocation of a wide range of toxic effector ..."
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Cited by 4 (2 self)
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These authors contributed equally to this work. The bacterial type VI secretion system (T6SS) is a large multi-component, dynamic macromolecular machine that plays an important role in the ecology of many Gram negative bacteria. T6SS is responsible for translocation of a wide range of toxic effector molecules allowing predatory cells to kill both prokaryotic as well as eukaryotic prey cells1-5. The T6SS organelle is functionally analogous to contractile tails of bacteriophages and is thought to attack cells by initially penetrating them with a trimeric protein complex called the VgrG spike6,7. Neither the exact protein composition of the T6SS organelle nor the mechanisms of effector selection and delivery are known. Here we report that proteins from the PAAR (Proline-Alanine-Alanine-aRginine) repeat superfamily form a sharp conical extension on the VgrG spike, which is further involved in attaching effector domains to the spike. The crystal structures of two PAAR-repeat proteins bound to VgrG-like partners show that these proteins function to sharpen the tip of the VgrG spike. We demonstrate that PAAR proteins are essential for T6SS- mediated secretion and target cell killing by Vibrio cholerae and Acinetobacter baylyi. Our results suggest a new model of the T6SS organelle in which the VgrG-PAAR spike complex is decorated with multiple effectors that are delivered simultaneously into target cells in a single contraction-driven translocation event. Correspondence and requests for materials should be addressed to P.G.L. (petr.leiman@epfl.ch) or J.J.M.
