Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions

No abstract is available for this paper.

• Publication year

  2007

• Venue

  Bioinform.

• Publication date

  Unknown publication date

• Fields of study

  Biology, Medicine, Computer Science, Environmental Science

• Identifiers
  DOI 10.1093/bioinformatics/btl547PMID 17077096
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Rice genetics IV

  2008cited by this paper
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  2005cited by this paper
• Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species.

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  1999cited by this paper
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  1999cited by this paper
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  1998cited by this paper
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  1997cited by this paper
• Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.)

  1997cited by this paper
• Microsatellite instability in yeast: dependence on the length of the microsatellite.

  1997influential reference
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  1997cited by this paper
• Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.)

  1996cited by this paper
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  1996cited by this paper
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  1991cited by this paper
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  1989cited by this paper
• Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.

  1987cited by this paper
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  1987cited by this paper
• Evolutionary relationships in the Sativa group of Oryza based on isozyme data

  1985cited by this paper
• The number of repeats expected in random nucleic acid sequences and found in genes

  1981cited by this paper
• The number of repeats expected in random nucleic acid sequences and found in genes.

  1981cited by this paper

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