RepeatAround: A software tool for finding and visualizing repeats in circular genomes and its application to a human mtDNA database

Mitochondrion

Volumn 6, Issue 4, 2006, Pages 218-224

  Goios, Ana ^a   Meirinhos, José ^a   Rocha, Ricardo ^a,b   Lopes, Ricardo ^a,b   Amorim, António ^a   Pereira, Luísa ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b LIACC Laboratório de Inteligência Artificial e Ciências de Computadores   (Portugal)

Author keywords

Circular genomes; Complementary repeats; Direct repeats; Inverted repeats; Mirror repeats

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; COMPUTER PROGRAM; DATA BASE; DATA EXTRACTION; GENBANK; GENE DELETION; GENE STRUCTURE; GENOME; HUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; STATISTICAL ANALYSIS; UNINDEXED SEQUENCE;

COMPUTATIONAL BIOLOGY; DNA, CIRCULAR; DNA, MITOCHONDRIAL; GENOMICS; HUMANS; REPETITIVE SEQUENCES, NUCLEIC ACID; SOFTWARE;

EID: 33748180150     PISSN: 15677249     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mito.2006.06.001     Document Type: Article

References (10)

1. Andrews R.M., Kubacka I., Chinnery P.F., Lightowlers R.N., Turnbull D.M., and Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23 (1999) 147
2. Brandon M.C., Lott M.T., Nguyen K.C., Spolim S., Navathe S.B., Baldi P., and Wallace D.C. MITOMAP: a human mitochondrial genome database-2004 update. Nucleic Acids Res. 33 Database Issue (2005) D611-D613
3. Chuzhanova N., Abeysinghe S.S., Krawczak M., and Cooper D.N. Translocation and gross deletion breakpoints in human inherited disease and cancer II: potential involvement of repetitive sequence elements in secondary structure formation between DNA ends. Hum. Mutat. 22 (2003) 245-251
4. Goios A., Nogueira C., Pereira C., Vilarinho L., Amorim A., and Pereira L. mtDNA single macrodeletions associated with myopathies: absence of haplogroup-related increased risk. J. Inherit. Metab. Dis. 28 (2005) 769-778
5. Gusfield D. Algorithms on Strings, Trees and Sequences (1997), Cambridge University Press, New York
6. Ingman M., Kaessmann H., Paabo S., and Gyllensten U. Mitochondrial genome variation and the origin of modern humans. Nature 408 (2000) 708-713
7. Kurtz S., and Schleiermacher C. REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics 15 (1999) 426-427
8. Mishmar D., Ruiz-Pesini E., Golik P., Macaulay V., Clark A.G., Hosseini S., Brandon M., Easley K., Chen E., Brown M.D., Sukernik R.I., Olckers A., and Wallace D.C. Natural selection shaped regional mtDNA variation in humans. Proc. Natl. Acad. Sci. USA 100 (2003) 171-176
9. Samuels D.C. Mitochondrial DNA repeats constrain the life span of mammals. Trends Genet. 20 (2004) 226-229
10. Samuels D.C., Schon E.A., and Chinnery P.F. Two direct repeats cause most human mtDNA deletions. Trends Genet. 20 (2004) 393-398