Searching microsatellites in DNA sequences: Approaches used and tools developed

Physiology and Molecular Biology of Plants

Volumn 18, Issue 1, 2012, Pages 11-19

  Grover, Atul ^a,b   Aishwarya, Veenu ^a,c   Sharma, P C ^a  

^a GURU GOBIND SINGH INDRAPRASTHA UNIVERSITY   (India)

^b Defence Institute of Bio Energy Research   (India)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Deterministic approaches; Microsatellites; Mining tools; Stochastic models

Indexed keywords

EID: 84856392690     PISSN: 09715894     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12298-011-0098-y     Document Type: Review

References (70)

1. Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27: 617-631.
2. Bagshaw ATM, Pitt JPW, Gemmell NJ (2006) Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots. BMC Genomics 7: 179.
3. Bagshaw ATM, Pitt JPW, Gemmell NJ (2008) High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots. BMC Genomics 9: 49.
4. Bai X, Zhang W, Ornates L, Jun T, Mittapalli O, Mian MAR, Michael AP (2010) Combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, Aphis glycines. PLoS One 5: e11370.
5. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: 573-580.
6. Benson G (2005) Tandem cyclic alignment. Discret Appl Math 146: 124-133.
7. Benson G, Waterman MS (1994) A method for fast database search for all k-nucleotide repeats. Nucleic Acids Res 22: 4828-4836.
8. Bilgen M, Karaca M, Onus AN, Ince AG (2004) A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences. Bioinformatics 20: 3379-3386.
9. Bizzaro JW, Marx KA (2003) Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA. BMC Bioinforma 4: 22.
10. Boeva V, Regnier M, Papatsenko D, Makeev V (2006) Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinformatics 22: 676-684.
11. Brodzik AK (2007) Quaternionic periodicity transform: an algebraic solution to the tandem repeat detection problem. Bioinformatics 23: 694-700.
12. Buchner M, Janjarasjitt S (2003) Detection and visualization of tandem repeats in DNA sequences. IEEE Trans Signal Process 51: 2280-2287.
13. Castelo AT, Martins W, Gao GR (2002) TROLL: Tandem repeats occurrence locator. Bioinformatics 18: 634-636.
14. Coward E, Dablos M (1998) Detecting periodic patterns in biological sequences. Bioinformatics 14: 498-507.
15. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Rev Genet 12: 499-510.
16. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Saijberg SL (1999) Alignment of whole genomes. Nucleic Acids Res 27: 2369-2376.
17. Delgrange O, Rivals E (2004) STAR: an algorithm to search for approximate tandem repeats. Bioinformatics 20: 2812-2820.
18. Dieringer D, Schlotterer C (2003) Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species. Genome Res 13: 2242-2251.
19. Du L, Zhou H, Yan H (2007) OMWSA: detection of DNA repeats using moving window spectral analysis. Bioinformatics 23: 631-633.
20. Eckert KA, Hile SE (2009) Every microsatellite is different: Intrinsic DNA features dictate mutagenesis of common microsatellites present in the human genome. Mol Carcinog 48: 379-388.
21. Emanuele VA, Tran TT, Zhou GT (2005) A Fourier product method for detecting approximate tandem repeats in DNA. Proceedings of the 13th Workshop on Statistical Signal Processing IEEE/SP 2005, 1390-1395.
22. Faircloth BC (2008) MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol Ecol Resour 8: 92-94.
23. Fischetti VA, Landau GM, Sellers PH, Schmidt JP (1993) Identifying periodic occurrences of a template with applications to protein structure. Inf Proc Lett 45: 11-18.
24. Fujimori S, Washio T, Higo K, Ohmoto Y, Murakami K, Matsubara K, Kawal J, Carnici P, Hayashizaki K, Kikuchi S, Tomita M (2003) A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett 554: 17-22.
25. Garg R, Patel RK, Tyagi AK, Jain M (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18: 53-63.
26. Grover A, Sharma PC (2011) Is spatial occurrence of microsatellites in the genome a determinant of their function and dynamics contributing to genome evolution? Curr Sci 100: 859-869.
27. Guichoux E, Lagache L, Wagner S, Chaumeil P, Léger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ (2011) Current trends in microsatellite genotyping. Mol Ecol Resour 11: 591-611.
28. Guo WJ, Ling J, Li P (2009) Consensus features of microsatellite distribution: Microsatellite contents are universally correlated with recombination rates and are preferentially depressed by centromeres in multicellular eukaryotic genomes. Genomics 93: 323-331.
29. Gupta R, Sarthi D, Mittal A, Singh K (2006) Exactly periodic subspace decomposition based approach for identifying tandem repeats in DNA sequences. http://www. eurasip. org/Proceedings/Eusipco/Eusipco2006/papers/1568981857. pdf.
30. Gupta R, Sarthi D, Mittal A, Singh K (2007) A novel signal processing measure to identify exact and inexact tandem repeat patterns in DNA sequences. EURASIP J. Bioinforma Syst Biol 2007: article ID 43596 doi: 10. 1155/2007/43596.
31. Hammock EAD, Young LJ (2005) Microsatellite instability generates diversity in brain and sociobehavioral traits. Science 308: 1630-1634.
32. Huda A, Marino-Ramirez L, Landsman D, Jordan King I (2009) Repetitive DNA elements, nucleosome binding and human gene expression. Gene 436: 12-22.
33. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
34. Karaca M, Bilgen M, Onus AN, Ince AG, Elmasulu SY (2005) Exact Tandem Repeats Analyzer (E-TRA): A new program for DNA sequence mining. J Genet 84: 49-54.
35. Karlin S, Morris M, Ghandour G, Leung MY (1988) Efficient algorithms for molecular sequence analysis. Proc Natl Acad Sci USA 85: 841-845.
36. Katti MV, Ranjekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18: 1161-1167.
37. Kofler R, Schlotterer C, Lelley T (2007) SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics 23: 1683-1685.
38. Kolpakov R, Bana G, Kucherov G (2003) mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 31: 3672-367.
39. Kraemer L, Beszteri B, Gabler-Schwarz S, Held C, Leese F, Mayer C, Pohlmann K, Frickenhaus S (2009) STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design. BMC Bioinformatics 10: 41.
40. Krishnan A, Tang F (2004) Exhaustive whole-genome tandem repeats search. Bioinformatics 20: 2702-2710.
41. Kurtz S, Schleiermacher C (1999) REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics 15: 426-427.
42. Kurtz S, Choudhuri JV, Ohlebusch E, Schlelermacher C, Stoye J, Giegerich R (2001) REPuter: the manifold applications of repeat analysis on genomic scale. Nucleic Acids Res 29: 4633-4642.
43. La Rota M, Kantety RV, Yu JK, Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat and barley. BMC Genomics 6: 23.
44. Leese F, Mayer C, Held C (2008) isolation of microsatellites from unknown genomes using known genomes as enrichment templates. Limnol Oceanogr Methods 7: 412-426.
45. Magain N, Forrest LL, Sérusiaux E, Goffinet B (2010) Microsatellite primers in the Peltigera dolichorhiza complex (lichenized ascomycete, Peltigerales). Am J Bot 97: e102-e104.
46. Merkel A, Gemmell N (2008) Detecting short tandem repeats from genome data: opening the software black box. Brief Bioinform 9: 355-366.
47. Mikheyev AS, Vo T, Wee B, Singer MC, Parmesan C (2010) Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: Performance and a comparison with AFLP-derived distances. PLoS One 5: e11212.
48. Mudunuri SB, Nagarajaram HA (2007) IMEx: Imperfect Microsatellite Extractor. Bioinformatics 23: 1181-1187.
49. Muresan DD, Parks TW (2003) Orthogonal exactly periodic subspace decomposition. IEEE Trans Signal Process 51: 2270-2279.
50. O'Dushlaine CT, Shields DC (2006) Tools for the identification of variable and potentially variable tandem repeats. BMC Genomics 7: 290.
51. Parisi V, Fonzo VD, Aluf-Pentini F (2003) STRING: finding tandem repeats in DNA sequences. Bioinformatics 19: 1733-1738.
52. Perry JC, Rowe L (2010) Rapid microsatellite development for water striders by next-generation sequencing. Journal of Hered 102: 125-129.
53. Pop PG (2006) Spectral techniques in finding DNA approximate tandem repeats. IEEE Int Conf Autom Qual Test Robot Cluj-Napoca Rom 2: 441-446.
54. Reneker J, Shyu CR, Zeng P, Polacco JC, Gassmann W (2004) ACMES: fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval. Nucleic Acids Res 32: W649-W653.
55. Sagot M, Myers E (1998) Identifying satellites in nucleic acid sequences. Proc Second Annu Int Conf Computat Mol Biol N Y pp. 234-242.
56. Santana QC, Coetzee MPA, Steenkamp ET, Mlonyeni OX, Hammond GNA, Wingfield MJ, Wingfield BD (2009) Microsatellite discovery by deep sequencing of enriched genomic libraries. BioTechniques 46: 217-2235.
57. Sethares WA, Staley TW (1999) Periodicity transform. IEEE Trans Signal Process 47: 2953-2964.
58. Sharma D, Issac B, Raghava GP, Ramaswamy R (2004) Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinformatics 20: 1405-1412.
59. Sharma PC, Grover A, Kahl G (2007) Mining microsatellites in eukaryotic genomes. Trends Biotechnol 25: 490-498.
60. Sobreira TJP, Durham AM, Gruber A (2006) TRAP: automated classification, quantification and annotation of tandemly repeated sequences. Bioinformatics 22: 361-362.
61. Sokol D, Benson G, Tojeira J (2007) Tandem repeats over the edit distance. Bioinformatics 23: e23-e30.
62. Sureshkumar S, Todesco M, Schneeberger K, Harilal R, Balasubramanian S, Weigel D (2009) A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana. Science 323: 1060.
63. Taneda A (2004) Adplot: detection and visualization of repetitive patterns in complete genomes. Bioinformatics 20: 701-708.
64. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.). Theor Appl Genet 106: 411-422.
65. Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10: 967-981.
66. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellites in plants: features and applications. Trends Biotechnol 23: 48-55.
67. Volfovsky N, Haas BJ, Salzberg SL (2001) A clustering method for repeat analysis in DNA sequences. Genome Biol 2: research0027. 1.
68. Wexler Y, Yakhini Z, Kashi Y, Geiger D (2004) Finding approximate tandem repeats in genomic sequences. Proc. 8th Annual Int Conf Res Comput Mol Biol (RECOMB04) pp 223-232.
69. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11: 1-16.
70. Zhou H, Du L, Yan H (2009) Detection of tandem repeats in DNA sequences based on parametric spectral estimation. IEEE Trans Inf Technol Biomed 13: 747-755.