what can blast do?
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What can BLAST do?. What can DiaGrid do better?. What can we do best?. What can BLAST do?. BLAST : Basic Local Alignment Search Tool. - PowerPoint PPT PresentationTRANSCRIPT
What can BLAST do?
What can DiaGrid do better?
What can we do best?
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
What can BLAST do?
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
Speed Accuracy
For web users: more than 100Mb query sequences;For sever users: nearly 50,000 computer processors .
What can DiaGrid do better?
Data Description Program Time
Data Size Database Blastall 2 Days
1Gb short reads;13,674,128 fasta sequences;Each length: 45bp
Private, 4.5Mb;35,692 fasta sequences;Each length: 100bp
DiaGrid4 hours (More CPU can be used)
Research Interests
Comparative, structural and functional genomics of soybean, Brassica genomes
Genome annotation of transposable elements and genome evolution
Centromere evolution
What can we do best?
B. napus
B. rapa
B. carinata
B. oleracea
B. juncea B. nigra
BBCC
CC
BB
AA
AACC
AABB
(N=18)
(N=10) (N=9)
(N=17)(N=8)
(N=19)
Triangleof U
Research Projects
Note: B. means Brasscia
progenitor
B.rapa (AA ) B.oleracea (CC )
B.napus (AACC)
4 MYA
500 ~ 10000 YA
1. The evolution of these two Brassica diploid species and and their tetraploid genome based on transposable elements;
2. Centromere evolution of the three neighboring Brassica species.
BLAST on DiaGrid
Transposable elements annotation
Identify TE polymorphism
Remove redundant Map reads which contain TE ends to the assembled genome
Hopes for the online version1. 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