WFRF:(Holmes K V)
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| Fältnamn | Indikatorer | Metadata |
|---|---|---|
| 000 | 06434naa a2201357 4500 | |
| 001 | oai:DiVA.org:uu-15807 | |
| 003 | SwePub | |
| 008 | 080306s2007 | |||||||||||000 ||eng| | |
| 024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-158072 URI |
| 024 | 7 | a https://doi.org/10.1101/gr.60343072 DOI |
| 040 | a (SwePub)uu | |
| 041 | a engb eng | |
| 042 | 9 SwePub | |
| 072 | 7 | a ref2 swepub-contenttype |
| 072 | 7 | a art2 swepub-publicationtype |
| 100 | 1 | a Margulies, Elliott H4 aut |
| 245 | 1 0 | a Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome |
| 264 | c 2007-06-13 | |
| 264 | 1 | b Cold Spring Harbor Laboratory,c 2007 |
| 338 | a print2 rdacarrier | |
| 520 | a A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization. | |
| 653 | a Animals | |
| 653 | a Evolution | |
| 653 | a Molecular | |
| 653 | a Genome | |
| 653 | a Human | |
| 653 | a Human Genome Project | |
| 653 | a Humans | |
| 653 | a Mammals/*genetics | |
| 653 | a Open Reading Frames | |
| 653 | a Phylogeny | |
| 653 | a Sequence Alignment | |
| 653 | a MEDICINE | |
| 653 | a MEDICIN | |
| 700 | 1 | a Cooper, Gregory M4 aut |
| 700 | 1 | a Asimenos, George4 aut |
| 700 | 1 | a Thomas, Daryl J4 aut |
| 700 | 1 | a Dewey, Colin N4 aut |
| 700 | 1 | a Siepel, Adam4 aut |
| 700 | 1 | a Birney, Ewan4 aut |
| 700 | 1 | a Keefe, Damian4 aut |
| 700 | 1 | a Schwartz, Ariel S4 aut |
| 700 | 1 | a Hou, Minmei4 aut |
| 700 | 1 | a Taylor, James4 aut |
| 700 | 1 | a Nikolaev, Sergey4 aut |
| 700 | 1 | a Montoya-Burgos, Juan I4 aut |
| 700 | 1 | a Löytynoja, Ari4 aut |
| 700 | 1 | a Whelan, Simon4 aut |
| 700 | 1 | a Pardi, Fabio4 aut |
| 700 | 1 | a Massingham, Tim4 aut |
| 700 | 1 | a Brown, James B4 aut |
| 700 | 1 | a Bickel, Peter4 aut |
| 700 | 1 | a Holmes, Ian4 aut |
| 700 | 1 | a Mullikin, James C4 aut |
| 700 | 1 | a Ureta-Vidal, Abel4 aut |
| 700 | 1 | a Paten, Benedict4 aut |
| 700 | 1 | a Stone, Eric A4 aut |
| 700 | 1 | a Rosenbloom, Kate R4 aut |
| 700 | 1 | a Kent, W James4 aut |
| 700 | 1 | a Bouffard, Gerard G4 aut |
| 700 | 1 | a Guan, Xiaobin4 aut |
| 700 | 1 | a Hansen, Nancy F4 aut |
| 700 | 1 | a Idol, Jacquelyn R4 aut |
| 700 | 1 | a Maduro, Valerie V B4 aut |
| 700 | 1 | a Maskeri, Baishali4 aut |
| 700 | 1 | a McDowell, Jennifer C4 aut |
| 700 | 1 | a Park, Morgan4 aut |
| 700 | 1 | a Thomas, Pamela J4 aut |
| 700 | 1 | a Young, Alice C4 aut |
| 700 | 1 | a Blakesley, Robert W4 aut |
| 700 | 1 | a Muzny, Donna M4 aut |
| 700 | 1 | a Sodergren, Erica4 aut |
| 700 | 1 | a Wheeler, David A4 aut |
| 700 | 1 | a Worley, Kim C4 aut |
| 700 | 1 | a Jiang, Huaiyang4 aut |
| 700 | 1 | a Weinstock, George M4 aut |
| 700 | 1 | a Gibbs, Richard A4 aut |
| 700 | 1 | a Graves, Tina4 aut |
| 700 | 1 | a Fulton, Robert4 aut |
| 700 | 1 | a Mardis, Elaine R4 aut |
| 700 | 1 | a Wilson, Richard K4 aut |
| 700 | 1 | a Clamp, Michele4 aut |
| 700 | 1 | a Cuff, James4 aut |
| 700 | 1 | a Gnerre, Sante4 aut |
| 700 | 1 | a Jaffe, David B4 aut |
| 700 | 1 | a Chang, Jean L4 aut |
| 700 | 1 | a Lindblad-Toh, Kerstinu Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi4 aut0 (Swepub:uu)kerli865 |
| 700 | 1 | a Lander, Eric S4 aut |
| 700 | 1 | a Hinrichs, Angie4 aut |
| 700 | 1 | a Trumbower, Heather4 aut |
| 700 | 1 | a Clawson, Hiram4 aut |
| 700 | 1 | a Zweig, Ann4 aut |
| 700 | 1 | a Kuhn, Robert M4 aut |
| 700 | 1 | a Barber, Galt4 aut |
| 700 | 1 | a Harte, Rachel4 aut |
| 700 | 1 | a Karolchik, Donna4 aut |
| 700 | 1 | a Field, Matthew A4 aut |
| 700 | 1 | a Moore, Richard A4 aut |
| 700 | 1 | a Matthewson, Carrie A4 aut |
| 700 | 1 | a Schein, Jacqueline E4 aut |
| 700 | 1 | a Marra, Marco A4 aut |
| 700 | 1 | a Antonarakis, Stylianos E4 aut |
| 700 | 1 | a Batzoglou, Serafim4 aut |
| 700 | 1 | a Goldman, Nick4 aut |
| 700 | 1 | a Hardison, Ross4 aut |
| 700 | 1 | a Haussler, David4 aut |
| 700 | 1 | a Miller, Webb4 aut |
| 700 | 1 | a Pachter, Lior4 aut |
| 700 | 1 | a Green, Eric D4 aut |
| 700 | 1 | a Sidow, Arend4 aut |
| 710 | 2 | a Uppsala universitetb Institutionen för medicinsk biokemi och mikrobiologi4 org |
| 773 | 0 | t Genome Researchd : Cold Spring Harbor Laboratoryg 17:6, s. 760-774q 17:6<760-774x 1088-9051x 1549-5469 |
| 856 | 4 | u http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=17567995&dopt=Citation |
| 856 | 4 | u http://genome.cshlp.org/content/17/6/760.full.pdf |
| 856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-15807 |
| 856 | 4 8 | u https://doi.org/10.1101/gr.6034307 |
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