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Volumn 1006, Issue , 2013, Pages 101-120

Optimizing selection of microsatellite loci from 454 pyrosequencing via post-sequencing bioinformatic analyses

Author keywords

Microsatellite marker development; Molecular markers; Next generation sequencing

Indexed keywords

GENOMIC DNA; MICROSATELLITE DNA; REPETITIVE DNA;

EID: 84877144983     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-389-3_7     Document Type: Article
Times cited : (3)

References (22)
  • 1
    • 33645894192 scopus 로고    scopus 로고
    • Microsatellites for ecologists: A practical guide to using and evaluating microsatellite markers
    • Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: A practical guide to using and evaluating microsatellite markers. Ecol Lett 9:615-629
    • (2006) Ecol Lett , vol.9 , pp. 615-629
    • Selkoe, K.A.1    Toonen, R.J.2
  • 2
    • 84857225391 scopus 로고    scopus 로고
    • Isolating microsatellite loci: Looking back, looking ahead
    • doi: 10.1007/978- 1-61779-228-1-12 .
    • Andrés JA, Bogdanowicz SM (2011) Isolating microsatellite loci: looking back, looking ahead. In: Methods in molecular biology, vol 772. Part 3, pp 211-232, doi: 10.1007/978- 1-61779-228-1-12 .
    • (2011) Methods In Molecular Biology , vol.772 , Issue.PART 3 , pp. 211-232
    • Andrés, J.A.1    Bogdanowicz, S.M.2
  • 4
    • 84877134386 scopus 로고    scopus 로고
    • July 27, 1996 Laboratory of Molecular Systematics-MRC 534. MSC Smithsonian Institution, Washington, DC 20560
    • Glenn TC (1996) The microsatellite manual version 6, July 27, 1996 Laboratory of Molecular Systematics - MRC 534. MSC Smithsonian Institution, Washington, DC 20560
    • (1996) Microsatellite Manual Version , vol.6
    • Glenn, T.C.1
  • 6
    • 19944396462 scopus 로고    scopus 로고
    • Isolating microsatellite DNA loci
    • In Zimmer EA, Roalson E (eds, part B.Academic Press, San Diego, USA
    • Glenn TC, Schable NA (2005) Isolating microsatellite DNA loci. In: Zimmer EA, Roalson E (eds) Molecular evolution: Producing the biochemical data, part B. Academic Press, San Diego, USA, pp 202-222
    • (2005) Molecular Evolution: Producing The Biochemical Data , pp. 202-222
    • Glenn, T.C.1    Schable, N.A.2
  • 7
    • 0036007439 scopus 로고    scopus 로고
    • Strategies for microsatellite isolation: A review
    • Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: A review. Mol Ecol 11:1-16
    • (2002) Mol Ecol , vol.11 , pp. 1-16
    • Zane, L.1    Bargelloni, L.2    Patarnello, T.3
  • 8
    • 0034767567 scopus 로고    scopus 로고
    • Microsatellite evolution in vertebrates: Inference from AC dinucleotide repeats
    • Neff BD, Gross MR (2001) Microsatellite evolution in vertebrates: Inference from AC dinucleotide repeats. Evolution 55:1717-1733
    • (2001) Evolution , vol.55 , pp. 1717-1733
    • Neff, B.D.1    Gross, M.R.2
  • 9
    • 79953131579 scopus 로고    scopus 로고
    • Twelve microsatellite markers in the invasive tunicate, Didemnum vexillum, isolated from low genome coverage 454 pyrosequencing reads
    • Abbott CL, Ebert D, Tabata A et al (2010) Twelve microsatellite markers in the invasive tunicate, Didemnum vexillum, isolated from low genome coverage 454 pyrosequencing reads. Conserv Genet Resour 3:79-81
    • (2010) Conserv Genet Resour , vol.3 , pp. 79-81
    • Abbott, C.L.1    Ebert, D.2    Tabata, A.3
  • 10
    • 77949335579 scopus 로고    scopus 로고
    • Rapid identi fi cation of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence
    • doi: 10.1111/j.1755-0998.2009.02750.x
    • Castoe TA, Poole AW, Gu W et al (2010) Rapid identi fi cation of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol Ecol Resour 10:341-347. doi: 10.1111/j.1755-0998.2009.02750.x
    • (2010) Mol Ecol Resour , vol.10 , pp. 341-347
    • Castoe, T.A.1    Poole, A.W.2    Gu, W.3
  • 11
    • 79959254890 scopus 로고    scopus 로고
    • Comparison of random and ssr-enriched shotgun pyrosequencing for microsatellite discovery and single multiplex pcr optimization in acacia harpophylla f
    • doi: 10.1111/j.1755- 0998.2011.03002.x
    • Lepais O, Bacles DFE (2011) Comparison of random and SSR-enriched shotgun pyrosequencing for microsatellite discovery and single multiplex PCR optimization in Acacia harpophylla F. Muell Ex Benth Mol Ecol Resour 11:711-724. doi: 10.1111/j.1755- 0998.2011.03002.x
    • (2011) Muell Ex Benth Mol Ecol Resour , vol.11 , pp. 711-724
    • Lepais, O.1    Bacles, D.F.E.2
  • 12
    • 79959250426 scopus 로고    scopus 로고
    • High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries
    • doi: 10.1111/j.1755- 0998.2011.02992.x
    • Malausa T, Gilles A, Meglecz E et al (2011) High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Mol Ecol Resour 11:638-644. doi: 10.1111/j.1755- 0998.2011.02992.x
    • (2011) Mol Ecol Resour , vol.11 , pp. 638-644
    • Malausa, T.1    Gilles, A.2    Meglecz, E.3
  • 13
    • 78650479127 scopus 로고    scopus 로고
    • Rapid microsatellite development for water striders by next-generation sequencing
    • doi: 10.1093/jhered/esq099
    • Perry JC, Rowe L (2011) Rapid microsatellite development for water striders by next-generation sequencing. J Hered 102(1):125-129. doi: 10.1093/jhered/esq099
    • (2011) J Hered , vol.102 , Issue.1 , pp. 125-129
    • Perry, J.C.1    Rowe, L.2
  • 14
    • 84877126327 scopus 로고    scopus 로고
    • Development of 38 microsatellite loci from the Arceye hawk fi sh, Paracirrhites arcatus, using next-generation sequencing and cross-ampli fi cation in other Cirrhitid species
    • doi: 10.1007/s12686-011-9589
    • Whitney JL, Karl SA (2012) Development of 38 microsatellite loci from the Arceye hawk fi sh, Paracirrhites arcatus, using next-generation sequencing and cross-ampli fi cation in other Cirrhitid species. Cons Genet Resour. doi: 10.1007/s12686-011-9589-
    • (2012) Cons Genet Resour.
    • Whitney, J.L.1    Karl, S.A.2
  • 15
    • 84877117654 scopus 로고    scopus 로고
    • Roche Technical Bulletin No 2010-010 August 2010 Multiplex Identi fi er (MID)
    • Roche Technical Bulletin No. 2010-010 August 2010 Multiplex Identi fi er (MID) Adaptors for Rapid Library Preparations. http://ftp.genome. o u e d u / p u b / 4 5 4 / T C B - 1 0 0 1 0 - MIDAdaptorsforRapidLibraryPreparations.pdf 16. SFF-EXTRACT and CLEAN-READS (http://bioinf. comav.upv.es/).
    • Adaptors for Rapid Library Preparations.
  • 16
    • 84874604550 scopus 로고    scopus 로고
    • FASTX-TOOLKIT (http://hannonlab.cshl.edu/ fastx-toolkit/).
    • Fastx-Toolkit
  • 17
    • 84890568804 scopus 로고    scopus 로고
    • FASTQC (http://www.bioinformatics.bbsrc. ac.uk/projects/fastqc/).
    • Fastqc
  • 18
    • 77949515434 scopus 로고    scopus 로고
    • QDD: A user-friendly program to select microsatellite markers and design primers from large sequencing projects
    • doi: 10.1093/bioinformatics/ btp670
    • Megelcz E, Costedoat C, Dubut V et al (2010) QDD: A user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26(3):403-404. doi: 10.1093/bioinformatics/ btp670, http://gsite.univ-provence.fr/ gsite/Local/egee/dir/meglecz/QDD.html
    • (2010) Bioinformatics , vol.26 , Issue.3 , pp. 403-404
    • Megelcz, E.1    Costedoat, C.2    Dubut, V.3
  • 19
    • 33750831582 scopus 로고    scopus 로고
    • Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
    • Kohany O, Gentles AJ, Hankus L et al (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 25(7):474, http://www. girinst.org/repbase/index.html
    • (2006) BMC Bioinformatics , vol.25 , Issue.7 , pp. 474
    • Kohany, O.1    Gentles, A.J.2    Hankus, L.3
  • 21
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365-386, http://frodo.wi.mit.edu
    • (2000) Methods Mol Biol , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.