%0 Journal Article %J Genome Res %D 2007 %T 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. %A Miller, Webb %A Rosenbloom, Kate %A Hardison, Ross C %A Hou, Minmei %A Taylor, James %A Raney, Brian %A Burhans, Richard %A King, David C %A Baertsch, Robert %A Blankenberg, Daniel %A Kosakovsky Pond, Sergei L %A Nekrutenko, Anton %A Giardine, Belinda %A Harris, Robert S %A Tyekucheva, Svitlana %A Diekhans, Mark %A Pringle, Thomas H %A Murphy, William J %A Lesk, Arthur %A Weinstock, George M %A Lindblad-Toh, Kerstin %A Gibbs, Richard A %A Lander, Eric S %A Siepel, Adam %A Haussler, David %A Kent, W James %K Animals %K Base Sequence %K Cats %K Cattle %K Codon, Initiator %K Codon, Terminator %K Conserved Sequence %K Databases, Genetic %K Dogs %K Genome, Human %K Guinea Pigs %K Humans %K Mice %K Molecular Sequence Data %K Mutagenesis, Insertional %K Rabbits %K Rats %K Sequence Alignment %K Sequence Deletion %X

This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006 assembly) at http://genome.ucsc.edu, downloaded in bulk by anonymous FTP from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way, or analyzed with the Galaxy server at http://g2.bx.psu.edu. This article illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. First, we present several vignettes involving insertions and deletions within protein-coding regions, including a look at some human-specific indels. Then we study the extent to which start codons and stop codons in the human sequence are conserved in other species, showing that start codons are in general more poorly conserved than stop codons. Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability. Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions.

%B Genome Res %V 17 %P 1797-808 %8 2007 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/17984227?dopt=Abstract %R 10.1101/gr.6761107 %0 Journal Article %J Nature %D 2005 %T Generation and annotation of the DNA sequences of human chromosomes 2 and 4. %A Hillier, LaDeana W %A Graves, Tina A %A Fulton, Robert S %A Fulton, Lucinda A %A Pepin, Kymberlie H %A Minx, Patrick %A Wagner-McPherson, Caryn %A Layman, Dan %A Wylie, Kristine %A Sekhon, Mandeep %A Becker, Michael C %A Fewell, Ginger A %A Delehaunty, Kimberly D %A Miner, Tracie L %A Nash, William E %A Kremitzki, Colin %A Oddy, Lachlan %A Du, Hui %A Sun, Hui %A Bradshaw-Cordum, Holland %A Ali, Johar %A Carter, Jason %A Cordes, Matt %A Harris, Anthony %A Isak, Amber %A van Brunt, Andrew %A Nguyen, Christine %A Du, Feiyu %A Courtney, Laura %A Kalicki, Joelle %A Ozersky, Philip %A Abbott, Scott %A Armstrong, Jon %A Belter, Edward A %A Caruso, Lauren %A Cedroni, Maria %A Cotton, Marc %A Davidson, Teresa %A Desai, Anu %A Elliott, Glendoria %A Erb, Thomas %A Fronick, Catrina %A Gaige, Tony %A Haakenson, William %A Haglund, Krista %A Holmes, Andrea %A Harkins, Richard %A Kim, Kyung %A Kruchowski, Scott S %A Strong, Cynthia Madsen %A Grewal, Neenu %A Goyea, Ernest %A Hou, Shunfang %A Levy, Andrew %A Martinka, Scott %A Mead, Kelly %A McLellan, Michael D %A Meyer, Rick %A Randall-Maher, Jennifer %A Tomlinson, Chad %A Dauphin-Kohlberg, Sara %A Kozlowicz-Reilly, Amy %A Shah, Neha %A Swearengen-Shahid, Sharhonda %A Snider, Jacqueline %A Strong, Joseph T %A Thompson, Johanna %A Yoakum, Martin %A Leonard, Shawn %A Pearman, Charlene %A Trani, Lee %A Radionenko, Maxim %A Waligorski, Jason E %A Wang, Chunyan %A Rock, Susan M %A Tin-Wollam, Aye-Mon %A Maupin, Rachel %A Latreille, Phil %A Wendl, Michael C %A Yang, Shiaw-Pyng %A Pohl, Craig %A Wallis, John W %A Spieth, John %A Bieri, Tamberlyn A %A Berkowicz, Nicolas %A Nelson, Joanne O %A Osborne, John %A Ding, Li %A Meyer, Rekha %A Aniko Sabo %A Shotland, Yoram %A Sinha, Prashant %A Wohldmann, Patricia E %A Cook, Lisa L %A Hickenbotham, Matthew T %A Eldred, James %A Williams, Donald %A Jones, Thomas A %A She, Xinwei %A Ciccarelli, Francesca D %A Izaurralde, Elisa %A Taylor, James %A Schmutz, Jeremy %A Myers, Richard M %A Cox, David R %A Huang, Xiaoqiu %A McPherson, John D %A Mardis, Elaine R %A Clifton, Sandra W %A Warren, Wesley C %A Chinwalla, Asif T %A Eddy, Sean R %A Marra, Marco A %A Ovcharenko, Ivan %A Furey, Terrence S %A Miller, Webb %A Eichler, Evan E %A Bork, Peer %A Suyama, Mikita %A Torrents, David %A Waterston, Robert H %A Wilson, Richard K %K Animals %K Base Composition %K Base Sequence %K Centromere %K Chromosomes, Human, Pair 2 %K Chromosomes, Human, Pair 4 %K Conserved Sequence %K CpG Islands %K Euchromatin %K Expressed Sequence Tags %K Gene Duplication %K Genetic Variation %K Genomics %K Humans %K Molecular Sequence Data %K Physical Chromosome Mapping %K Polymorphism, Genetic %K Primates %K Proteins %K Pseudogenes %K Recombination, Genetic %K RNA, Messenger %K RNA, Untranslated %K Sequence Analysis, DNA %X

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.

%B Nature %V 434 %P 724-31 %8 2005 Apr 07 %G eng %N 7034 %1 https://www.ncbi.nlm.nih.gov/pubmed/15815621?dopt=Abstract %R 10.1038/nature03466