What can BLAST do? What can DiaGrid do better? What can we do best?
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
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
What can DiaGrid do better? Speed Accuracy For web users: more than 100Mb query sequences; For sever users: nearly 50,000 computer processors .
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
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
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)
Transposable elements annotation Identify TE polymorphism BLAST on DiaGrid Map reads which contain TE ends to the assembled genome Remove redundant
Hopes for the online version • 1. Containing all NCBI BLAST contains
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