BWtrs: A tool for searching for tandem repeats in DNA sequences based on the Burrows-Wheeler transform

Genomics

Volumn 96, Issue 5, 2010, Pages 316-321

  Pokrzywa, Rafal ^a   Polanski, Andrzej ^a,b  

^a SILESIAN UNIVERSITY OF TECHNOLOGY   (Poland)

^b POLISH JAPANESE INSTITUTE OF INFORMATION TECHNOLOGY   (Poland)

Author keywords

Block sorting; Burrows Wheeler Transform (BWT); Microsatellites; Repetitive DNA; Tandem repeat

Indexed keywords

DINUCLEOTIDE; DNA; TRINUCLEOTIDE;

ARTICLE; BURROWS WHEELER TRANSFORM ALGORITHM; CHICKEN; CHIMPANZEE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DNA SEQUENCE; GENETIC ALGORITHM; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; INTERNET; MATHEMATICAL ANALYSIS; MOUSE; NONHUMAN; ONLINE SYSTEM; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TANDEM REPEAT;

ALGORITHMS; ANIMALS; BASE SEQUENCE; CHICKENS; COMPUTATIONAL BIOLOGY; GENOME, HUMAN; HUMANS; INTERNET; SOFTWARE; TANDEM REPEAT SEQUENCES;

EID: 78649445430     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2010.08.001     Document Type: Article

References (40)

1. Ellegren H. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 2004, 5:435-445.
2. Denoeud F., Vergnaud G., Benson G. Predicting human minisatellite polymorphism. Genome Res. 2003, 13:856-867.
3. Verstrepen K.J., Jansen A., Lewitter F., Fink G.R. Intragenic tandem repeats generate functional variability. Nat. Genet. 2005, 37:986-990.
4. Gatchel J.R., Zoghbi H.Y. Diseases of unstable repeat expansion: mechanisms and common principles. Nat. Rev. Genet. 2005, 6:743-755.
5. Gill P., Kimpton C.P., Urquhart A., Oldroyd N., Millican E.S., Watson S.K., Downes T.J. Automated short tandem repeat (STR) analysis in forensic casework - a strategy for the future. Electrophoresis 2005, vol. 16(1):1543-1552.
6. Yuan B., Vaske D., Weber J.L., Beck J., Sheffield V.C. Improved set of short-tandem-repeat polymorphisms for screening the human genome. Am. J. Hum. Genet. 1997, vol. 60(2):459-460.
7. Parson W., Kirchebner R., Mühlmann R., Renner K., Kofler A., Schmidt S., Kofler R. Cancer cell line identification by short tandem repeat profiling: power and limitations. FASEB J. 2005, 19(3):434-436.
8. Pelotti S., Ceccardi S., Alu M., Lugaresi F., Trane R., Falconi M., Bini C., Cicognani A. Cancerous tissues in forensic genetic analysis. Genet. Test. 2008, 11(4):397-400.
9. Ames D., Murphy N., Helentjaris T., Sun N., Chandler V. Comparative analyses of human single- and multilocus tandem repeats. Genetics 2008, 179:1693-1704.
10. Brandstrom M., Ellegren H. Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias. Genome Res. 2008, 18(6):881-887.
11. Kimmel M., Xu H., Fu X.Y., Renwick A., Chakraborty R. Microsatellite variation: effects of natural selection, population structure, and demographic changes of population size. Am. J. Hum. Genet. 2002, 61.
12. Alba M.M., Laskowski R.A., Hancock J.M. Detecting cryptically simple protein sequences using the SIMPLE algorithm. Bioinformatics 2002, 18:672-678.
13. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999, 27:573-580.
14. Bizzaro J.W., Marx K.A. Poly: a quantitative analysis tool for simple se-quence repeat (SSR) tracts in DNA. BMC Bioinform. 2003, 4:22.
15. Hancock J.M., Armstrong J.S. SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences. Comput. Appl. Biosci. 1994, 10:67-70.
16. Kolpakov R., Bana G., Kucherov G. mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res. 2003, 31(13):3672-3678.
17. Smit A.F.A., Hubley R., Green P. RepeatMasker Open-3.0. 1996-2004 1996, .
18. Merkel A., Gemmell N. Detecting short tandem repeats from genome data: opening the software black box. Brief. Bioinform. 2008, 9(5):355-366.
19. Leclercq S., Rivals E., Jarne P. Detecting microsatellites within genomes: significant variation among algorithms. BMC Bioinform. 2007, vol. 8:125.
20. Burrows M., Wheeler D.J. A block-sorting lossless data compression algorithm. SRC Research Report 124 May 10 1994, Digital Equipment Corporation, Palo Alto, California.
21. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 2009, 25(14):1754-1760.
22. Pokrzywa R. Application of the Burrows-Wheeler Transform for searching for tandem repeats in DNA sequences. Int. J. Bioinform. Res. Appl. 2009, vol. 5(4):432-446.
23. Ferragina P., Manzini G. Opportunistic data structures with applications. Proceedings of the 41st Annual Symposium on Foundations of Computer Science 2000, 390-398.
24. Abajian, C., http://espressosoftware.com/sputnik/index.html.
25. Stoye J., Gusfield D. Simple and flexible detection of contiguous repeats using a suffix tree. Lecture Notes in Computer Science 1998, 1448:140-152.
26. Abouelhoda M.I., Kurtz S., Ohlebusch E. The enhanced suffix array and its applications to genome analysis. WABI 2002. LNCS 2002, 2452:449-463.
27. Kurtz S. The Vmatch large scale sequence analysis software. Center for Bioinformatics 2003, Center for Bioinformatics, Univ. of Hamburg.
28. Kolpakov R., Kucherov G. Finding maximal repetitions in a word in linear time. Proceedings of the 40th Annual Symposium on Foundations of Computer Science 1999, 596-604.
29. Nomenclature committee of the international union of biochemistry (NC-IUB) Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences. Eur. J. Biochem. 1985, 150:1-5.
30. Morgante M., Hanafey M., Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet. 2002, 30:194-200.
31. La Rota M., Kantety R.V., Yu J.K., Sorrells M.E. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 2005, 18(6(1)):23.
32. Manber U., Myers E.W. Suffix array: a new method for on-line string searches. SIAM J. Comput. 1993, 22:935-948.
33. Karkkainen J. Fast BWT in small space by blockwise suffix sorting. Theor. Comput. Sci. 2007, 87(3):249-257.
34. Hon W.-K., Lam T.-W., Sadakane K., Sung W.-K., Yiu S.-M. A space and time efficient algorithm for constructing compressed suffix arrays. Algorithmica 2007, 48:23-36.
35. NCBI - FASTA format description, http://www.ncbi.nlm.nih.gov/blast/fasta.shtml.
36. EFetch - Entrez Programming Utilities, http://www.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html.
37. Kruglyak S., Durrett R.T., Schug M.D., Aquadro C.F. Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc. Natl Acad. Sci. 1998, 95:10774-10778.
38. Bell G.I., Jurka J. The length distribution of perfect dimer repetitive DNA is consistent with its evolution by an unbiased single-step mutation process. J. Mol. Evol. 1997, 44:414-421.
39. Dieringer D., Schlotterer C. Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species. Genome Res. 2003, 13:2242-2251.
40. Santibanez-Koref M.F., Gangeswaran R., Hancock J.M. A relationship between lengths of microsatellites and nearby substitution rates in mammalian genomes. Mol. Biol. Evol. 2001, 18:2119-2123.