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Parametric alignment of Drosophila genomes

Colin Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter
2005 PLoS Computational Biology  
Our main result is the construction of a whole genome parametric alignment of Drosophila melanogaster and Drosophila pseudoobscura.  ...  Citation: Dewey CN, Huggins PM, Woods K, Sturmfels B, Pachter L (2006) Parametric alignment of Drosophila genomes. PLoS Comput Biol 2(6): e73.  ...  Synopsis Dewey and colleagues describe a parametric alignment of the genomes of Drosophila melanogaster and Drosophila pseudoobscura.  ... 
doi:10.1371/journal.pcbi.0020073.eor fatcat:kkppbyl6zndktagrvwiz7igfeq

Parametric Alignment of Drosophila Genomes

Colin N. Dewey, Peter M. Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter
2006 PLoS Computational Biology  
Our main result is the construction of a whole genome parametric alignment of Drosophila melanogaster and Drosophila pseudoobscura.  ...  We demonstrate the utility of our parametric alignment for biological inference by showing that cis-regulatory elements are more conserved between Drosophila melanogaster and Drosophila pseudoobscura than  ...  Synopsis Dewey and colleagues describe a parametric alignment of the genomes of Drosophila melanogaster and Drosophila pseudoobscura.  ... 
doi:10.1371/journal.pcbi.0020073 pmid:16789815 pmcid:PMC1480539 fatcat:qrq66ady25aelhsaakfpgyqqyq

Evolution of the Phosphatase Gene Family Across Nematode Worms and Flies

Paulina Tsai, Melissa A. Wilson Sayres
2013 Berkeley scientific journal  
We conducted a phylogenetic analysis of all genes in the phosphatase gene family across nematodes and flies using sequences from a 6-way alignment of nematode worms and a 15way alignment of insects, including  ...  12 Drosophila species.  ...  This makes ML more powerful than both NJ and MP, non-parametric statistical methods (15) . We used PhyML to compute the Maximum Likelihood tree for each set of alignments.  ... 
doi:10.5070/bs3181020657 fatcat:z42zxvvzhfe4pmhvdtuxwghclm

Page 172 of Genetics Vol. 169, Issue 1 [page]

2005 Genetics  
Ruin, 2002 Compu- tational analysis of core promoters in the Drosophila genome. Genome Biol. 3: R87. OLIver, B., 2002 Genetic control of germline sex determination in Drosophila. Int. Rev.  ...  Vinson, 2004 Clustering of DNA sequences in human promoters. Genome Res. 14: 1562-1574. FLYBase, 2003 The FlyBase database of the Drosophila genome proj- ects and community literature.  ... 

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

Avinash Varadarajan, Robert K Bradley, Ian H Holmes
2008 Genome Biology  
Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data.  ...  Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks.  ...  alignments of 12 Drosophila genomes [20, 49] .  ... 
doi:10.1186/gb-2008-9-10-r147 pmid:18840304 pmcid:PMC2760874 fatcat:igmaipmpyvdbnb2u2h5xawh75q

Page 1397 of Genetics Vol. 177, Issue 3 [page]

2007 Genetics  
Molecular Evolution of Drosophila Chemoreceptors 1397 they were supported by, or not covered by, the syntenic assemblies.  ...  Nomenclature: After detailed discussion with several other research groups interested in Drosophila chemosensory genes (including the authors of DROSOPHILA ODORANT RECEPTOR NOMENCLATURE COMMITTEE 2000;  ... 

The Drosophila melanogaster methuselah Gene: A Novel Gene with Ancient Functions

Ana Rita Araújo, Micael Reis, Helder Rocha, Bruno Aguiar, Ramiro Morales-Hojas, Sandra Macedo-Ribeiro, Nuno A. Fonseca, David Reboiro-Jato, Miguel Reboiro-Jato, Florentino Fdez-Riverola, Cristina P. Vieira, Jorge Vieira (+1 others)
2013 PLoS ONE  
We also show that, in D. americana (a species of the virilis group of Drosophila), a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time,  ...  The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth), has been described as a novel gene that is less than 10 million years old.  ...  The inferred phylogenetic relationships obtained with two different alignments (ClustalW2 and MUSCLE) of 143 Drosophila mth-like gene sequences retrieved from the 12 annotated Drosophila genomes, are shown  ... 
doi:10.1371/journal.pone.0063747 pmid:23696853 pmcid:PMC3655951 fatcat:4dkoubpxybehjktaxzszao4wl4

Parametric k-best alignment [article]

Peter Huggins, Ruriko Yoshida
2008 arXiv   pre-print
Thus parametric k-best alignment is tractable, and can be applied at the whole-genome scale like parametric alignment.  ...  Thus we extend parametric alignment to parametric k-best alignment, which asks for all possible k-tuples of k-best alignment summaries (s_1, s_2, ..., s_k), as well as the k-best optimality region of scoring  ...  Parametric alignment has enjoyed remarkably good complexity results, enabling whole-genome parametric analysis of Drosophila genomes [4] .  ... 
arXiv:0809.1473v1 fatcat:bq5xnh5qrbajjirc3dhnowix54

Evolutionary Modeling and Prediction of Non-Coding RNAs in Drosophila

Robert K. Bradley, Andrew V. Uzilov, Mitchell E. Skinner, Yuri R. Bendaña, Lars Barquist, Ian Holmes, Robert Belshaw
2009 PLoS ONE  
We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene.  ...  We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment.  ...  Acknowledgments We thank Adam Siepel, Simon Prochnik, Benedict Paten and Marcin Joachimiak for helpful comments on the preparation of this manuscript.  ... 
doi:10.1371/journal.pone.0006478 pmid:19668382 pmcid:PMC2721679 fatcat:zlh25sg7erehzd4qptegzlfrwi

A Non-Parametric Peak Calling Algorithm for DamID-Seq

Renhua Li, Leonie U. Hempel, Tingbo Jiang, Jindan Yu
2015 PLoS ONE  
genome.  ...  technology to the fat body tissue of Drosophila, followed by deep sequencing (DamID-Seq).  ...  Emily Clough for generating most of the DamID-Seq data. Author Contributions Conceived and designed the experiments: RL TJ. Performed the experiments: RL LH. Analyzed the data: RL LH.  ... 
doi:10.1371/journal.pone.0117415 pmid:25785608 pmcid:PMC4364623 fatcat:3h7rdoxihzdpdogpehmh7uz7q4

A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster

V. Stolc
2004 Science  
We used a maskless photolithography method to produce DNA oligonucleotide microarrays with unique probe sequences tiled throughout the genome of Drosophila melanogaster and across predicted splice junctions  ...  Comparison to genome-wide RNA interference data and to gene annotations revealed distinguishable levels of expression for different classes of genes and higher levels of expression for genes with essential  ...  We used the whole-genome BLASTZ alignment between D. melanogaster and D. pseudoobscura of (25) to classify each base pair within our NEP probes as aligned (i.e., belonging to a chromosomal region with  ... 
doi:10.1126/science.1101312 pmid:15499012 fatcat:acg3nedqhzhrtjto4c3ix3bizy

Genomic signatures of globally enhanced gene duplicate accumulation in the megadiverse higher Diptera fueling intralocus sexual conflict resolution

Riyue Bao, Markus Friedrich
2020 PeerJ  
Focusing on close to 6,000 insect core gene families containing maximally six paralogs, we detected a conspicuously higher number of lineage-specific duplications in Drosophila (689) compared to Anopheles  ...  fly Drosophila melanogaster (Diptera: Brachycera), the mosquito Anopheles gambiae (Diptera: Culicomorpha), the red flour beetle Tribolium castaneum (Coleoptera), and the honeybee Apis mellifera (Hymenoptera  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj.10012 pmid:33083121 pmcid:PMC7560327 fatcat:p7ok74ojpraf5dbkf43k7wwrc4

Identifying Conserved Genomic Elements and Designing Universal Probe Sets To Enrich Them [article]

Brant C Faircloth
2016 bioRxiv   pre-print
Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic, and population genetic studies.  ...  of the Arachnid probe set as part of a separate manuscript (Starrett et al.  ...  I would also like to thank the Baylor College of Medicine Human Genome Sequencing Center (http://www.hgsc.bcm.tmc.edu), who have made all of the data generated as part of the i5k Initiative (i5K Consortium  ... 
doi:10.1101/077172 fatcat:sdawcrnrdzfv3pz55gru572sdm

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster

A. K. Holloway, D. J. Begun, A. Siepel, K. S. Pollard
2008 Genome Research  
Acknowledgments We thank Angie Hinrichs at UCSC for providing the 15-way whole-genome MULTIZ alignments, Ryan Bickel and Mia Levine at UC Davis for valuable comments and suggestions, Melissa Eckert at  ...  UC Davis for laboratory advice and assistance, Elizabeth Milano and Umbreen Arshad at UC Davis for laboratory assistance, and Hiram Clawson at UCSC for help with installation of the Kent library.  ...  Results Using whole-genome alignments of 10 Drosophila species to the D. melanogaster reference (Karolchik et al. 2003 (Karolchik et al. , 2004 Blanchette et al. 2004) , we identified genomic regions  ... 
doi:10.1101/gr.077131.108 pmid:18583644 pmcid:PMC2556263 fatcat:ujo7kv3sxbdrpoorhz23zrkose

Molecular Evolution of the Drosophila Retinome: Exceptional Gene Gain in the Higher Diptera

R. Bao, M. Friedrich
2009 Molecular biology and evolution  
Using genomic information from mosquito, red flour beetle, honeybee, mouse, and sea anemone, we have studied the molecular evolution of 91 Drosophila genes involved in eye primordium determination, retinal  ...  However, all three functional groups contain a conspicuous fraction of evolutionarily younger genes, which originated by tandem duplication in the lineage leading to Drosophila, whereas gene duplications  ...  Parametric Bootstrap Analysis Amino acid sequence alignments were simulated with PSeq-Gen (Rambaut and Grassly 1997) along the assumed opsin gene tree shown in figure 4 applying the JTT model of sequence  ... 
doi:10.1093/molbev/msp039 pmid:19252076 fatcat:jij4kzbji5fzzocm2vnzdm7w5q
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