TY - JOUR AU - Lander, E. S. AU - Linton, L. M. AU - Birren, B. AU - Nusbaum, C. AU - Zody, M. C. AU - Baldwin, J. AU - Devon, K. AU - Dewar, K. AU - Doyle, M. AU - FitzHugh, W. PY - 2001 DA - 2001// TI - Initial sequencing and analysis of the human genome JO - Nature VL - 409 UR - https://doi.org/10.1038/35057062 DO - 10.1038/35057062 ID - Lander2001 ER - TY - JOUR AU - Han, J. S. AU - Szak, S. T. AU - Boeke, J. D. PY - 2004 DA - 2004// TI - Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes JO - Nature VL - 429 UR - https://doi.org/10.1038/nature02536 DO - 10.1038/nature02536 ID - Han2004 ER - TY - JOUR AU - Fondon, J. W. AU - Garner, H. R. PY - 2004 DA - 2004// TI - Molecular origins of rapid and continuous morphological evolution JO - PNAS VL - 101 UR - https://doi.org/10.1073/pnas.0408118101 DO - 10.1073/pnas.0408118101 ID - Fondon2004 ER - TY - JOUR AU - Singer, M. F. PY - 1982 DA - 1982// TI - SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes JO - Cell VL - 28 UR - https://doi.org/10.1016/0092-8674(82)90194-5 DO - 10.1016/0092-8674(82)90194-5 ID - Singer1982 ER - TY - CHAP AU - Singer, M. AU - Berg, P. PY - 1991 DA - 1991// BT - Genes and Genomes PB - University Science Books CY - Mill Valley, California ID - Singer1991 ER - TY - JOUR AU - Bennett, E. A. AU - Coleman, L. E. AU - Tsui, C. AU - Pittart, W. S. AU - Devine, S. E. PY - 2004 DA - 2004// TI - Natural genetic variation caused by transposable elements in humans JO - Genetics VL - 168 UR - https://doi.org/10.1534/genetics.104.031757 DO - 10.1534/genetics.104.031757 ID - Bennett2004 ER - TY - JOUR AU - Nekrutenko, A. AU - Li, W. -. H. PY - 2001 DA - 2001// TI - Transposable elements are found in a large number of human protein-coding genes JO - Trends in Genetics VL - 17 UR - https://doi.org/10.1016/S0168-9525(01)02445-3 DO - 10.1016/S0168-9525(01)02445-3 ID - Nekrutenko2001 ER - TY - JOUR AU - Deininger, P. L. AU - Batzer, M. A. PY - 2002 DA - 2002// TI - Mammalian retroelements JO - Genome Research VL - 12 UR - https://doi.org/10.1101/gr.282402 DO - 10.1101/gr.282402 ID - Deininger2002 ER - TY - JOUR AU - Holmes, I. PY - 2002 DA - 2002// TI - Transcendent elements: whole-genome transposon screens and open evolutionary questions JO - Genome Research VL - 12 UR - https://doi.org/10.1101/gr.453102 DO - 10.1101/gr.453102 ID - Holmes2002 ER - TY - JOUR AU - Bao, Z. AU - Eddy, S. R. PY - 2002 DA - 2002// TI - Automated de novo identification of repeat sequence families in sequenced genomes JO - Genome Research VL - 12 UR - https://doi.org/10.1101/gr.88502 DO - 10.1101/gr.88502 ID - Bao2002 ER - TY - JOUR AU - Campagna, D. AU - Romualdi, C. AU - Vitulo, N. AU - Del Favero, M. AU - Lexa, M. AU - Cannata, N. AU - Valle, G. PY - 2005 DA - 2005// TI - RAP: a new computer program for de novo identification of repeated sequences in whole genomes JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti039 DO - 10.1093/bioinformatics/bti039 ID - Campagna2005 ER - TY - JOUR AU - Price, A. L. AU - Jones, N. C. AU - Pevzner, P. A. PY - 2005 DA - 2005// TI - De novo identification of repeat families in large genomes JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1018 DO - 10.1093/bioinformatics/bti1018 ID - Price2005 ER - TY - JOUR AU - Edgar, R. C. AU - Myers, E. W. PY - 2005 DA - 2005// TI - PILER: identification and classification of genomic repeats JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1003 DO - 10.1093/bioinformatics/bti1003 ID - Edgar2005 ER - TY - JOUR AU - Taneda, A. PY - 2004 DA - 2004// TI - Adplot: detection and visualization of repetitive patterns in complete genomes JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg470 DO - 10.1093/bioinformatics/btg470 ID - Taneda2004 ER - TY - JOUR AU - Caspi, A. AU - Pachter, L. PY - 2006 DA - 2006// TI - Identification of transposable elements using multiple alignments of related genomes JO - Genome Research VL - 16 UR - https://doi.org/10.1101/gr.4361206 DO - 10.1101/gr.4361206 ID - Caspi2006 ER - TY - JOUR AU - Quesneville, H. AU - Bergman, C. M. AU - Andrieu, O. AU - Autard, D. AU - Nouaud, D. AU - Ashburner, M. AU - Anxolabehere, D. PY - 2005 DA - 2005// TI - Combined evidence annotation of transposable elements in genome sequences JO - PLoS Comp Biol VL - 1 UR - https://doi.org/10.1371/journal.pcbi.0010022 DO - 10.1371/journal.pcbi.0010022 ID - Quesneville2005 ER - TY - STD TI - Smit AFA, Hubley R, Green P: RepeatMasker Open-3.0. 1996–2004, [http://www.repeatmasker.org] UR - http://www.repeatmasker.org ID - ref17 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - STD TI - The Ensembl archive of swine (Sus scrofa) sequences. [ftp://ftp.ensembl.org/pub/traces/sus_scrofa/fasta/] UR - ftp://ftp.ensembl.org/pub/traces/sus_scrofa/fasta/ ID - ref19 ER - TY - STD TI - The Gene Index Project. [http://compbio.dfci.harvard.edu/tgi/] UR - http://compbio.dfci.harvard.edu/tgi/ ID - ref20 ER - TY - JOUR AU - Pevzner, P. A. AU - Tang, H. AU - Tesler, G. PY - 2004 DA - 2004// TI - De novo repeat classification and fragment assembly JO - Genome Research VL - 14 UR - https://doi.org/10.1101/gr.2395204 DO - 10.1101/gr.2395204 ID - Pevzner2004 ER - TY - JOUR AU - Zhi, D. AU - Raphael, B. J. AU - Price, A. L. AU - Tang, H. AU - Pevzner, P. A. PY - 2006 DA - 2006// TI - Identifying repeat domains in large genomes JO - Genome Biology VL - 7 UR - https://doi.org/10.1186/gb-2006-7-1-r7 DO - 10.1186/gb-2006-7-1-r7 ID - Zhi2006 ER - TY - JOUR AU - Shedlock, A. M. AU - Okada, N. PY - 2000 DA - 2000// TI - SINE insertions: powerful tools for molecular systematics JO - BioEssays VL - 22 UR - https://doi.org/3.0.CO;2-Z DO - 3.0.CO;2-Z ID - Shedlock2000 ER - TY - JOUR AU - Shimamura, M. AU - Abe, H. AU - Nikaido, M. AU - Ohshima, K. AU - Okada, N. PY - 1999 DA - 1999// TI - Geneology of families of SINEs in Cetaceans and Artiodactyls: The presence of a huge superfamily of tRNAGLU-derived families of SINEs JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026194 DO - 10.1093/oxfordjournals.molbev.a026194 ID - Shimamura1999 ER - TY - STD TI - NCBI BLAST cow sequences. [http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9913] UR - http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9913 ID - ref25 ER - TY - STD TI - Bovine Genome Project. [http://www.hgsc.bcm.tmc.edu/projects/bovine/] UR - http://www.hgsc.bcm.tmc.edu/projects/bovine/ ID - ref26 ER - TY - STD TI - The R Project for Statistical Computing. [http://www.r-project.org/] UR - http://www.r-project.org/ ID - ref27 ER - TY - STD TI - BAC PAC Resources, Children's Hospital Oakland Research Institute (CHORI). [http://bacpac.chori.org/mporcine44.htm] UR - http://bacpac.chori.org/mporcine44.htm ID - ref28 ER - TY - JOUR AU - Hafez, E. E. AU - Ghany, A. G. A. A. AU - Zaki, E. A. PY - 2006 DA - 2006// TI - LTR- retrotransposons-based molecular markers in cultivated Egyptian cottons G. barbadense L JO - African Journal of Biotechnology VL - 5 ID - Hafez2006 ER - TY - STD TI - Comparative Vertebrate Sequencing Initiative. [http://www.nisc.nih.gov/] UR - http://www.nisc.nih.gov/ ID - ref30 ER - TY - JOUR AU - Cooper, G. M. AU - Stone, E. A. AU - Asimenos, G. AU - Green, E. D. AU - Batzoglou, S. AU - Sidow, A. PY - 2005 DA - 2005// TI - Distribution and intensity of constraint in mammalian genomic sequence JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3577405 DO - 10.1101/gr.3577405 ID - Cooper2005 ER - TY - CHAP AU - Korf, I. AU - Yandell, M. AU - Bedell, J. PY - 2003 DA - 2003// BT - BLAST ID - Korf2003 ER - TY - STD TI - RECON software package. [http://selab.janelia.org/recon.html] UR - http://selab.janelia.org/recon.html ID - ref33 ER - TY - CHAP AU - Rozen, S. AU - Skaletsky, H. J. ED - Krawetz, S. ED - Misener, S. PY - 2000 DA - 2000// TI - Primer3 on the WWW for general users and for biologist programmers BT - Bioinformatics Methods and Protocols Methods in Molecular Biology PB - Humana Press CY - Totowa, NJ ID - Rozen2000 ER -