Alignathon: A competitive assessment of whole genome alignment methods
暂无分享,去创建一个
David Haussler | Inna Dubchak | Brian J. Raney | Dent Earl | Benedict Paten | Michael Brudno | Glenn Hickey | Aaron E. Darling | Hiram Clawson | Minmei Hou | Victor V. Solovyev | Javier Herrero | Carsten Kemena | Alexander Poliakov | Ionas Erb | Jia-Ming Chang | Stephen Fitzgerald | Ngan Nguyen | Robert S. Harris | Kathryn Beal | Igor Seledtsov | Vladimir Molodtsov | Jaebum Kim | Jian Ma | Cedric Notredame
[1] Daniel J. Blankenberg,et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. , 2007, Genome research.
[2] G. Gonnet,et al. ALF—A Simulation Framework for Genome Evolution , 2011, Molecular biology and evolution.
[3] Ian Holmes,et al. Dynamic programming alignment accuracy , 1998, RECOMB '98.
[4] C. Notredame,et al. Using multiple alignment methods to assess the quality of genomic data analysis. , 2003 .
[5] Andrew D. Smith,et al. SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution , 2005, BMC Bioinformatics.
[6] Jian Ma,et al. PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling - (Extended Abstract) , 2011, RECOMB.
[7] Cory L. Strope,et al. indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels. , 2006, Molecular biology and evolution.
[8] Robert G. Beiko,et al. A simulation test bed for hypotheses of genome evolution , 2007, Bioinform..
[9] Benedict Paten,et al. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment , 2009, Bioinform..
[10] B. Birren,et al. Sequencing and comparison of yeast species to identify genes and regulatory elements , 2003, Nature.
[11] F. Blattner,et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.
[12] Dan Graur,et al. Local Reliability Measures from Sets of Co-Optimal Multiple Sequence Alignments , 2007, Pacific Symposium on Biocomputing.
[13] Andreas Wilm,et al. An enhanced RNA alignment benchmark for sequence alignment programs , 2006, Algorithms for Molecular Biology.
[14] Lior Pachter,et al. VISTA: computational tools for comparative genomics , 2004, Nucleic Acids Res..
[15] Albert J. Vilella,et al. A high-resolution map of human evolutionary constraint using 29 mammals , 2011, Nature.
[16] Jian Ma,et al. PSAR-Align: improving multiple sequence alignment using probabilistic sampling , 2014, Bioinform..
[17] ENCODEConsortium,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[18] Folker Meyer,et al. Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions , 1997, ISMB.
[19] Colin N. Dewey,et al. Aligning multiple whole genomes with Mercator and MAVID. , 2007, Methods in molecular biology.
[20] Steven Salzberg,et al. Mugsy: fast multiple alignment of closely related whole genomes , 2010, Bioinform..
[21] Antonio Carvajal-Rodríguez,et al. Simulation of Genes and Genomes Forward in Time , 2010, Current genomics.
[22] Elisabeth R. M. Tillier,et al. The accuracy of several multiple sequence alignment programs for proteins , 2006, BMC Bioinformatics.
[23] Inanç Birol,et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species , 2013, GigaScience.
[24] N. Perna,et al. progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement , 2010, PloS one.
[25] D. Haussler,et al. Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.
[26] Nuno A. Fonseca,et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. , 2011, Genome research.
[27] M. Suchard,et al. Alignment Uncertainty and Genomic Analysis , 2008, Science.
[28] D. Higgins,et al. Multiple sequence alignments. , 2005, Current opinion in structural biology.
[29] Lode Wyns,et al. SABmark- a benchmark for sequence alignment that covers the entire known fold space , 2005, Bioinform..
[30] Reed A. Cartwright,et al. DNA assembly with gaps (Dawg): simulating sequence evolution , 2005, Bioinform..
[31] Marc A. Martí-Renom,et al. Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package , 2013, Bioinform..
[32] Folker Meyer,et al. Rose: generating sequence families , 1998, Bioinform..
[33] Ophir Frieder,et al. On understanding and classifying web queries , 2006 .
[34] Desmond G. Higgins,et al. Analysis and Comparison of Benchmarks for Multiple Sequence Alignment , 2006, Silico Biol..
[35] Melanie A. Huntley,et al. Evolution of genes and genomes on the Drosophila phylogeny , 2007, Nature.
[36] Joshua M. Stuart,et al. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. , 2009, The Journal of heredity.
[37] Cédric Notredame,et al. Upcoming challenges for multiple sequence alignment methods in the high-throughput era , 2009, Bioinform..
[38] W. Miller,et al. Mulan: multiple-sequence local alignment and visualization for studying function and evolution. , 2005, Genome research.
[39] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[40] Rachel Kolodny,et al. Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. , 2005, Journal of molecular biology.
[41] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[42] David Haussler,et al. Cactus: Algorithms for genome multiple sequence alignment. , 2011, Genome research.
[43] Cédric Notredame,et al. Recent Evolutions of Multiple Sequence Alignment Algorithms , 2007, PLoS Comput. Biol..
[44] Olivier Poch,et al. BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark , 2005, Proteins.
[45] Mary Goldman,et al. The UCSC Genome Browser database: extensions and updates 2013 , 2012, Nucleic Acids Res..
[46] Michael J. Wise. No so HoT – heads or tails is not able to reliably compare multiple sequence alignments , 2010 .
[47] C. V. Jongeneel,et al. The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods , 2007, Nucleic Acids Res..
[48] Inna Dubchak,et al. Multiple whole-genome alignments without a reference organism. , 2009, Genome research.
[49] Colin N. Dewey,et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. , 2007, Genome research.
[50] Tal Pupko,et al. GUIDANCE: a web server for assessing alignment confidence scores , 2010, Nucleic Acids Res..
[51] Ian Holmes,et al. Evolutionary Modeling and Prediction of Non-Coding RNAs in Drosophila , 2009, PloS one.
[52] Tal Pupko,et al. An alignment confidence score capturing robustness to guide tree uncertainty. , 2010, Molecular biology and evolution.
[53] Carsten Wiuf,et al. Gene Genealogies, Variation and Evolution - A Primer in Coalescent Theory , 2004 .
[54] E. Birney,et al. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. , 2008, Genome research.
[55] Manuel Gil,et al. Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. , 2012, Methods in molecular biology.
[56] J. Wakeley. Coalescent Theory: An Introduction , 2008 .
[57] Susan J. Brown,et al. The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. , 2013, The Journal of heredity.
[58] Xiaoyu Chen,et al. Comparative assessment of methods for aligning multiple genome sequences , 2010, Nature Biotechnology.
[59] I. Holmes,et al. Tools for simulating evolution of aligned genomic regions with integrated parameter estimation , 2008, Genome Biology.