What can BLAST do?

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