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BLAST FOR GENOMICS

BLAST FOR GENOMICS. Jianxin Ma maj@purdue.edu Department of Agronomy Purdue University. Soybean Genome Sequencing Project DOE-JGI Community Sequencing Program Brassica Genome Sequencing Project BGI-Shenzhen, Chinese Academy of Agricultural Sciences. Why transposable elements?.

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BLAST FOR GENOMICS

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  1. BLASTFOR GENOMICS Jianxin Ma maj@purdue.edu Department of Agronomy Purdue University

  2. Soybean Genome Sequencing Project DOE-JGI Community Sequencing Program Brassica Genome Sequencing Project BGI-Shenzhen, Chinese Academy of Agricultural Sciences

  3. Why transposable elements? • Transposable elements (TEs), popularly called “jumping genes” are sequences of DNA that can move around to different chromosomal positions in a cell. • First TEs were discovered in maize in 1948 by Barbara McClintock Awarded the Nobel Prize in 1983 (1902-1992) • TEs make up a large fraction of genome sizes in most higher organisms: • TEs were often referred to be “molecular junk”, but are now recognized as important, even crucial parts of the blueprints of plants and animals: ~35% ~50%

  4. The Landscape of the Soybean Genome Schmutz et al., 2010, Nature

  5. 42% 157 families 353 families 16% 58% Du et al., 2010, BMC Genomics

  6. Structure-based analysis and Homology-based analysis (BLAST)

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