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Volumn 9, Issue 5, 2008, Pages 355-366

Detecting short tandem repeats from genome data: Opening the software black box

Author keywords

Algorithm; Comparison; Genome; Method; Microsatellite; Software; Tandem repeat

Indexed keywords

MICROSATELLITE DNA;

EID: 49949114192     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbn028     Document Type: Article
Times cited : (58)

References (56)
  • 2
    • 25844438495 scopus 로고    scopus 로고
    • Repeat instability: Mechanisms of dynamic mutations
    • Pearson CE, Edamura KN, Cleary JD. Repeat instability: Mechanisms of dynamic mutations. Nat Rev Genet 2005;6: 729-42.
    • (2005) Nat Rev Genet , vol.6 , pp. 729-742
    • Pearson, C.E.1    Edamura, K.N.2    Cleary, J.D.3
  • 3
    • 33646130830 scopus 로고    scopus 로고
    • Simple sequence repeats as advantageous mutators in evolution
    • Kashi Y, King DG. Simple sequence repeats as advantageous mutators in evolution. Trends Genet 2006;22: 253-9.
    • (2006) Trends Genet , vol.22 , pp. 253-259
    • Kashi, Y.1    King, D.G.2
  • 4
    • 0032615249 scopus 로고    scopus 로고
    • DNA microsatellites: Agents of evolution?
    • Moxon ER, Wills C. DNA microsatellites: Agents of evolution? Sci Am 1999;280:94-9.
    • (1999) Sci Am , vol.280 , pp. 94-99
    • Moxon, E.R.1    Wills, C.2
  • 5
    • 11144230088 scopus 로고    scopus 로고
    • Molecular origins of rapid and continuous morphological evolution
    • Fondon JW, Garner HR. Molecular origins of rapid and continuous morphological evolution. Proc Natl Acad Sci USA 2004;101 18058-63.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 18058-18063
    • Fondon, J.W.1    Garner, H.R.2
  • 6
    • 20644472668 scopus 로고    scopus 로고
    • Microsatellite instability generates diversity in brain and sociobehavioral traits
    • Hammock EAD, Young LJ. Microsatellite instability generates diversity in brain and sociobehavioral traits. Science 2005;308:1630-4.
    • (2005) Science , vol.308 , pp. 1630-1634
    • Hammock, E.A.D.1    Young, L.J.2
  • 8
    • 10744226741 scopus 로고    scopus 로고
    • Two distinct modes of microsatellite mutation processes: Evidence from the complete genomic sequences of nine species
    • Dieringer D, Schlotterer C. Two distinct modes of microsatellite mutation processes: Evidence from the complete genomic sequences of nine species. Genome Res 2003;13:2242-51.
    • (2003) Genome Res , vol.13 , pp. 2242-2251
    • Dieringer, D.1    Schlotterer, C.2
  • 9
    • 0034946803 scopus 로고    scopus 로고
    • Differential distribution of simple sequence repeats in eukaryotic genome sequences
    • Katti MV, Ranjekar PK, Gupta VS. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 2001;18:1161-7.
    • (2001) Mol Biol Evol , vol.18 , pp. 1161-1167
    • Katti, M.V.1    Ranjekar, P.K.2    Gupta, V.S.3
  • 10
    • 0036897944 scopus 로고    scopus 로고
    • Microsatellites: Genomic distribution, putative functions and mutational mechanisms: A review
    • Li YC, Korol AB, Fahima T, et al. Microsatellites: Genomic distribution, putative functions and mutational mechanisms: A review. Mol Ecol 2002;11:2453-65.
    • (2002) Mol Ecol , vol.11 , pp. 2453-2465
    • Li, Y.C.1    Korol, A.B.2    Fahima, T.3
  • 11
    • 2442701496 scopus 로고    scopus 로고
    • Microsatellites within genes: Structure, function, and evolution
    • Li YC, Korol AB, Fahima T, et al. Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 2004;21 991-1007.
    • (2004) Mol Biol Evol , vol.21 , pp. 991-1007
    • Li, Y.C.1    Korol, A.B.2    Fahima, T.3
  • 12
    • 4644359310 scopus 로고    scopus 로고
    • A comparison of the nature and abundance of microsatellites in 14 fungal genomes
    • Lim S, Notley-McRobb L, Lim M, et al. A comparison of the nature and abundance of microsatellites in 14 fungal genomes. Fungal Genet Biol 2004;41:1025-36.
    • (2004) Fungal Genet Biol , vol.41 , pp. 1025-1036
    • Lim, S.1    Notley-McRobb, L.2    Lim, M.3
  • 13
    • 0036478903 scopus 로고    scopus 로고
    • Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes
    • Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 2002;30:194-200.
    • (2002) Nat Genet , vol.30 , pp. 194-200
    • Morgante, M.1    Hanafey, M.2    Powell, W.3
  • 15
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson G. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res 1999;27:573-80.
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1
  • 17
    • 0036080338 scopus 로고    scopus 로고
    • Detecting cryptically simple protein sequences using the SIMPLE algorithm
    • Alba MM, Laskowski RA, Hancock JM. Detecting cryptically simple protein sequences using the SIMPLE algorithm. Bioinformatics 2002;18 672-8.
    • (2002) Bioinformatics , vol.18 , pp. 672-678
    • Alba, M.M.1    Laskowski, R.A.2    Hancock, J.M.3
  • 18
    • 0028118638 scopus 로고
    • SIMPLE34: An improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences
    • Hancock JM, Armstrong JS. 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.
    • (1994) Comput Appl Biosci , vol.10 , pp. 67-70
    • Hancock, J.M.1    Armstrong, J.S.2
  • 19
    • 34548383001 scopus 로고    scopus 로고
    • EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes
    • Aishwarya V, Grover A, Sharma PC. EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes. BMC Genomics 2007;8:225.
    • (2007) BMC Genomics , vol.8 , pp. 225
    • Aishwarya, V.1    Grover, A.2    Sharma, P.C.3
  • 20
    • 0035166931 scopus 로고    scopus 로고
    • STRBase: A short tandem repeat DNA database for the human identity testing community
    • Ruitberg CM, Reeder DJ, Butler JM. STRBase: A short tandem repeat DNA database for the human identity testing community. Nucleic Acids Res 2001;29:320-2.
    • (2001) Nucleic Acids Res , vol.29 , pp. 320-322
    • Ruitberg, C.M.1    Reeder, D.J.2    Butler, J.M.3
  • 21
    • 25444517281 scopus 로고    scopus 로고
    • COPASAAR-a database for proteomic analysis of single amino acid repeats
    • Depledge DP, Dalby AR. COPASAAR-a database for proteomic analysis of single amino acid repeats. BMC Bioinformatics 2005;6:196.
    • (2005) BMC Bioinformatics , vol.6 , pp. 196
    • Depledge, D.P.1    Dalby, A.R.2
  • 22
    • 33747119651 scopus 로고    scopus 로고
    • ProtRepeatsDB: A database of amino acid repeats in genomes
    • Kalita M, Ramasamy G, Duraisamy S, et al. ProtRepeatsDB: A database of amino acid repeats in genomes. BMC Bioinformatics 2006;7:336.
    • (2006) BMC Bioinformatics , vol.7 , pp. 336
    • Kalita, M.1    Ramasamy, G.2    Duraisamy, S.3
  • 23
    • 34249009076 scopus 로고    scopus 로고
    • Detecting microsatellites within genomes: Significant variation among algorithms
    • Leclercq S, Rivals E, Jarne P. Detecting microsatellites within genomes: significant variation among algorithms. BMC Bioinformatics 2007; 8:125.
    • (2007) BMC Bioinformatics , vol.8 , pp. 125
    • Leclercq, S.1    Rivals, E.2    Jarne, P.3
  • 24
    • 35648929376 scopus 로고    scopus 로고
    • Mining microsatellites in eukaryotic genomes
    • Sharma PC, Grover A, Kahl G. Mining microsatellites in eukaryotic genomes. Trends Biotechnol 2007;25:490-8.
    • (2007) Trends Biotechnol , vol.25 , pp. 490-498
    • Sharma, P.C.1    Grover, A.2    Kahl, G.3
  • 26
    • 23844525077 scopus 로고    scopus 로고
    • Repbase update, a database of eukaryotic repetitive elements
    • Jurka J, Kapitonov VV, Pavlicek A, et al. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005;110:462-7.
    • (2005) Cytogenet Genome Res , vol.110 , pp. 462-467
    • Jurka, J.1    Kapitonov, V.V.2    Pavlicek, A.3
  • 27
    • 49949098603 scopus 로고
    • Available at
    • Abajian C. Sputnik. 1994. Available at: http://espressosoftware.com/ pages/sputnik.jsp.
    • (1994)
    • Sputnik, A.C.1
  • 29
    • 0034882994 scopus 로고    scopus 로고
    • Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic market potential
    • Temnykh S, DeClerck G, Lukashova A, et al. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic market potential. Genome Res 2001;11:1441-52.
    • (2001) Genome Res , vol.11 , pp. 1441-1452
    • Temnykh, S.1    DeClerck, G.2    Lukashova, A.3
  • 30
    • 0037854629 scopus 로고    scopus 로고
    • Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
    • Thiel T, Michalek W, Varshney RK, et al. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 2003;106 411-22.
    • (2003) Theor Appl Genet , vol.106 , pp. 411-422
    • Thiel, T.1    Michalek, W.2    Varshney, R.K.3
  • 31
    • 2942580979 scopus 로고    scopus 로고
    • Poly: A quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA
    • Bizzaro JW, Marx KA. Poly: A quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA. BMC Bioinformatics 2003;4 22.
    • (2003) BMC Bioinformatics , vol.4 , pp. 22
    • Bizzaro, J.W.1    Marx, K.A.2
  • 32
    • 25444467752 scopus 로고    scopus 로고
    • Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley
    • La Rota M, Kantety RV, Yu JK, et al. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 2005;6:23.
    • (2005) BMC Genomics , vol.6 , pp. 23
    • La Rota, M.1    Kantety, R.V.2    Yu, J.K.3
  • 33
    • 34547852208 scopus 로고    scopus 로고
    • SciRoKo: A new tool for whole genome microsatellite search and investigation
    • Kofler R, Schlotterer C, Lelley T. SciRoKo: A new tool for whole genome microsatellite search and investigation. Bioinformatics 2007;23 1683-5.
    • (2007) Bioinformatics , vol.23 , pp. 1683-1685
    • Kofler, R.1    Schlotterer, C.2    Lelley, T.3
  • 34
    • 33645107183 scopus 로고    scopus 로고
    • Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression
    • Boeva V, Regnier M, Papatsenko D, et al. Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinformatics 2006;22:676-84.
    • (2006) Bioinformatics , vol.22 , pp. 676-684
    • Boeva, V.1    Regnier, M.2    Papatsenko, D.3
  • 35
    • 25644460030 scopus 로고    scopus 로고
    • Finding approximate tandem repeats in genomic sequences
    • Wexler Y, Yakhini Z, Kashi Y, et al. Finding approximate tandem repeats in genomic sequences. J Comput Biol 2005; 12:928-42.
    • (2005) J Comput Biol , vol.12 , pp. 928-942
    • Wexler, Y.1    Yakhini, Z.2    Kashi, Y.3
  • 36
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981;147:195-7.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 37
    • 0043123037 scopus 로고    scopus 로고
    • Efficient and flexible detection of tandem repeats in DNA
    • Kolpakov R, Bana G, Kucherov G. mreps: Efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 2003;31:3672-8.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3672-3678
    • Kolpakov, R.1    Bana, G.2    Kucherov, G.3    mreps4
  • 38
    • 0028070169 scopus 로고
    • The exact numbers of possible microsatellite motifs
    • Jin L, Zhong YX, Chakraborty R. The exact numbers of possible microsatellite motifs. Am J Hum Genet 1994;55: 582-3.
    • (1994) Am J Hum Genet , vol.55 , pp. 582-583
    • Jin, L.1    Zhong, Y.X.2    Chakraborty, R.3
  • 39
    • 0030895078 scopus 로고    scopus 로고
    • Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome
    • Freudenreich CH, Stavenhagen JB, Zakian VA. Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome. Mol Cell Biol 1997;17: 2090-8.
    • (1997) Mol Cell Biol , vol.17 , pp. 2090-2098
    • Freudenreich, C.H.1    Stavenhagen, J.B.2    Zakian, V.A.3
  • 40
    • 8844220452 scopus 로고    scopus 로고
    • STAR: An algorithm to search for tandem approximate repeats
    • Delgrange O, Rivals E. STAR: An algorithm to search for tandem approximate repeats. Bioinformatics 2004;20: 2812-20.
    • (2004) Bioinformatics , vol.20 , pp. 2812-2820
    • Delgrange, O.1    Rivals, E.2
  • 41
    • 85142193953 scopus 로고    scopus 로고
    • Mudunuri SB, Nagarajaram HA. IMEx: Imperfect microsatellite extractor. Bioinformatics 2007;23:1181-7.
    • Mudunuri SB, Nagarajaram HA. IMEx: Imperfect microsatellite extractor. Bioinformatics 2007;23:1181-7.
  • 42
    • 41049084843 scopus 로고    scopus 로고
    • Detecting microsatellites in genome data: Variance in definitions and bioinformatic approaches cause systematic bias
    • Merkel A, Gemmell N. Detecting microsatellites in genome data: Variance in definitions and bioinformatic approaches cause systematic bias. Evol Bioinform 2008;1-6.
    • (2008) Evol Bioinform , pp. 1-6
    • Merkel, A.1    Gemmell, N.2
  • 43
    • 38049048656 scopus 로고    scopus 로고
    • The genome-wide determinants of human and chimpanzee microsatellite evolution
    • Kelkar YD, Tyekucheva S, Chiaromonte F, et al. The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res 2008;18:30-8.
    • (2008) Genome Res , vol.18 , pp. 30-38
    • Kelkar, Y.D.1    Tyekucheva, S.2    Chiaromonte, F.3
  • 44
    • 10644294655 scopus 로고    scopus 로고
    • Genome-wide prediction of human VNTRs
    • Naslund K, Saetre P, von Salome J, et al. Genome-wide prediction of human VNTRs. Genomics 2005;85:24-35.
    • (2005) Genomics , vol.85 , pp. 24-35
    • Naslund, K.1    Saetre, P.2    von Salome, J.3
  • 45
    • 33745056327 scopus 로고    scopus 로고
    • Tandem repeat copy-number variation in protein-coding regions of human genes
    • O'Dushlaine CT, Edwards RJ, Park SD, et al. Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biol 2005;6:R69.
    • (2005) Genome Biol , vol.6
    • O'Dushlaine, C.T.1    Edwards, R.J.2    Park, S.D.3
  • 47
    • 0035890910 scopus 로고    scopus 로고
    • REPuter: The manifold applications of repeat analysis on a genomic scale
    • Kurtz S, Choudhuri JV, Ohlebusch E, et al. REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 2001;29:4633-42.
    • (2001) Nucleic Acids Res , vol.29 , pp. 4633-4642
    • Kurtz, S.1    Choudhuri, J.V.2    Ohlebusch, E.3
  • 48
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general user and for biologists programmers
    • Krawetz S, Misener S eds, Totowa, NJ: Humana Press
    • Rozen S, Skaletsky H. Primer3 on the WWW for general user and for biologists programmers. In: Krawetz S, Misener S (eds). Bioinformatics Methods and Protocols: Methods in Molecular Biology. Totowa, NJ: Humana Press, 2000, 365-86.
    • (2000) Bioinformatics Methods and Protocols: Methods in Molecular Biology , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 49
    • 33747854965 scopus 로고    scopus 로고
    • SSRPrimer and SSR taxonomy tree: Biome SSR discovery
    • Jewell E, Robinson A, Savage D, et al. SSRPrimer and SSR taxonomy tree: Biome SSR discovery. Nucleic Acids Res 2006;34:W656-9.
    • (2006) Nucleic Acids Res , vol.34
    • Jewell, E.1    Robinson, A.2    Savage, D.3
  • 50
    • 33751309415 scopus 로고    scopus 로고
    • Tools for the identification of variable and potentially variable tandem repeats
    • O'Dushlaine CT, Shields DC. Tools for the identification of variable and potentially variable tandem repeats. BMC Genomics 2006;7:290.
    • (2006) BMC Genomics , vol.7 , pp. 290
    • O'Dushlaine, C.T.1    Shields, D.C.2
  • 51
    • 0033855579 scopus 로고    scopus 로고
    • Repeat polymorphisms within gene regions: Phenotypic and evolutionary implications
    • Wren JD, Forgacs E, Fondon JW, et al. Repeat polymorphisms within gene regions: Phenotypic and evolutionary implications. Am J Hum Genet 2000;67:345-56.
    • (2000) Am J Hum Genet , vol.67 , pp. 345-356
    • Wren, J.D.1    Forgacs, E.2    Fondon, J.W.3
  • 54
    • 33846074290 scopus 로고    scopus 로고
    • InSatDb: A microsatellite database of fully sequenced insect genomes
    • Archak S, Meduri E, Kumar PS, et al. InSatDb: A microsatellite database of fully sequenced insect genomes. Nucleic Acids Res 2007;35:D36-9.
    • (2007) Nucleic Acids Res , vol.35
    • Archak, S.1    Meduri, E.2    Kumar, P.S.3
  • 55
    • 0038278603 scopus 로고    scopus 로고
    • An exhaustive DNA micro-satellite map of the human genome using high performance computing
    • Collins JR, Stephens RM, Gold B, et al. An exhaustive DNA micro-satellite map of the human genome using high performance computing. Genomics 2003;82:10-19.
    • (2003) Genomics , vol.82 , pp. 10-19
    • Collins, J.R.1    Stephens, R.M.2    Gold, B.3
  • 56
    • 15944382704 scopus 로고    scopus 로고
    • TRbase: A database relating tandem repeats to disease genes for the human genome
    • Boby T, Patch AM, Aves SJ. TRbase: A database relating tandem repeats to disease genes for the human genome. Bioinformatics 2005;21 811-16.
    • (2005) Bioinformatics , vol.21 , pp. 811-816
    • Boby, T.1    Patch, A.M.2    Aves, S.J.3


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