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What can BLAST do?

What can BLAST do?. What can DiaGrid do better?. What can we do best?. What can BLAST do?. BLAST : Basic Local Alignment Search Tool.

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What can BLAST do?

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  1. What can BLAST do? What can DiaGrid do better? What can we do best?

  2. What can BLAST do? BLAST: Basic Local Alignment Search Tool A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence • Identifying species • Locating domains • Establishing phylogeny • DNA mapping • Comparison

  3. FASTA and BLAST of alignment programs: • NCBI BLAST: blastn, blastp, blastx, tblastn, tblastx... • Mega BLAST: high similarity • WU-BLAST: sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases • SAM program, PSI-BLAST: slowly but surely find remote homologs • SSAHA: maps sequence reads to the genome with blazing efficiency • BLAT: mRNA/DNA and cross-species protein alignments

  4. What can DiaGrid do better? Speed Accuracy For web users: more than 100Mb query sequences; For sever users: nearly 50,000 computer processors .

  5. What can we do best? Research Interests • Comparative, structural and functional genomics of soybean, Brassica genomes • Genome annotation of transposable elements and genome evolution • Centromere evolution

  6. B. juncea B. nigra B. carinata AABB BB BBCC (N=18) (N=8) (N=17) Triangle of U B. rapa B. oleracea AA CC (N=10) (N=9) B. napus AACC (N=19) Research Projects Note: B. means Brasscia

  7. progenitor 4 MYA B.rapa (AA ) B.oleracea (CC ) • The evolution of these two Brassica diploid species and and their tetraploid genome based on transposable elements; • Centromere evolution of the three neighboring Brassica species. 500 ~ 10000 YA B.napus (AACC)

  8. Transposable elements annotation Identify TE polymorphism BLAST on DiaGrid Map reads which contain TE ends to the assembled genome Remove redundant

  9. Hopes for the online version • 1. Containing all NCBI BLAST contains

  10. 2. Upload private database • 3. Download the alignment • 4. More options for the web user like the command line input, especially E-Value, gap costs, filters, word size, and substitution matrix

  11. Thanks and enjoy your lunch!

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