Primates and mouse NumtS in the UCSC Genome Browser

BMC Bioinformatics

Volumn 13, Issue SUPPL.4, 2012, Pages

  Calabrese, Francesco Maria ^a   Simone, Domenico ^a   Attimonelli, Marcella ^a  

^a UNIVERSITY OF BARI   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE MAPPING; COMPARATIVE GENOMICS; GENOME BROWSERS; GENOME EVOLUTION; MAMMALIAN GENOMES; MITOCHONDRIAL DNA; NUCLEAR GENOMES; PCR AMPLIFICATION; PRESENCE/ABSENCE; STRESS EVENTS;

DNA; MAMMALS; POLYMERASE CHAIN REACTION;

GENES;

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CELL NUCLEUS; COMPUTER PROGRAM; GENETICS; GENOME; HUMAN; MITOCHONDRIAL GENE; MITOCHONDRION; MOUSE; PAN TROGLODYTES; RHESUS MONKEY;

ANIMALS; CELL NUCLEUS; DNA, MITOCHONDRIAL; GENES, MITOCHONDRIAL; GENOME; HUMANS; MACACA MULATTA; MICE; MITOCHONDRIA; PAN TROGLODYTES; SOFTWARE;

EID: 84864934013     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-S4-S15     Document Type: Article

References (21)

1. Gaziev AI, Shaǐkhaev GO. Nuclear mitochondrial pseudogenes. Mol Biol (Mosk) 2010, 44(3):405-417.
2. Hazkani-Covo E, Covo S. Numt-mediated double-strand break repair mitigates deletions during primate genome evolution. PLoS Genet 2008, 4(10):e1000834.
3. Hazkani-Covo E. Mitochondrial insertions into primate nuclear genomes suggest the use of numts as a tool for phylogeny. Mol Biol Evol 2009, 26(10):2175-2179. 10.1093/molbev/msp131, 19578158.
4. Jensen-Seaman MI, Wildschutte JH, Soto-Calderón ID, Anthony NM. A comparative approach shows differences in patterns of numt insertion during hominoid evolution. J Mol Evol 2009, 68(6):688-699. 10.1007/s00239-009-9243-4, 3140062, 19471988.
5. Hazkani-Covo E, Graur D. A comparative analysis of numt evolution in human and chimpanzee. Mol Biol Evol 2007, 24(1):13-18.
6. Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics 2011, 12(1):517. 10.1186/1471-2164-12-517, 3228558, 22013967.
7. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Neil H. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 1999, 23:147. 10.1038/13779, 10508508.
8. Hazkani-Covo E, Zeller RM, Martin W. Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet 2010, 6(2):e1000834. 10.1371/journal.pgen.1000834, 2820518, 20168995.
9. Richly E, Leister D. NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 2004, 21(6):1081-1084. 10.1093/molbev/msh110, 15014143.
10. UCSC Chromosomes Download Page. , ftp://hgdownload.cse.ucsc.edu/goldenPath/
11. Goecks J, Nekrutenko A, Taylor J, . Galaxy Team Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11(8):R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864, Galaxy Team.
12. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Current Protocols in Molecular Biology 2010, Chapter 19(Unit 19.10):1-21.
13. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005, 15(10):1451-1455. 10.1101/gr.4086505, 1240089, 16169926.
14. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12(6):996-1006. 186604, 12045153.
15. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res 2003, 13(1):103-107. 10.1101/gr.809403, 430961, 12529312.
16. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map (SAM) format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup.
17. UCSC Genome Browser Homepage. , http://genome.ucsc.edu/
18. Chimpanzee Custom Tracks. , http://genome.ucsc.edu/cgi-bin/hgTracks?db=panTro2&position=chrM&hgt.customText=http://dl.dropbox.com/u/31015858/all_PTR_tracks.txt
19. Rhesus Macaque Custom Tracks. , http://genome.ucsc.edu/cgi-bin/hgTracks?db=rheMac2&position=chr1:5484600-5484695&hgt.customText=http://dl.dropbox.com/u/31015858/all_MMU_tracks.txt
20. Calvignac S, Konecny L, Malard F, Douady CJ. Preventing the pollution of mitochondrial datasets with nuclear mitochondrial paralogs (numts). Mitochondrion 2011, 11(2):246-254. 10.1016/j.mito.2010.10.004, 21047564.
21. Primer-Blast Software. , http://www.ncbi.nlm.nih.gov/tools/primer-blast/