Tricking the Guard: Exploiting Plant Defense for Disease Susceptibility

From www.sciencemag.org - October 28, 4:06 PM 

Typically, pathogens deploy virulence effectors to disable defense. Plants defeat effectors with resistance proteins that guard effector targets. Here, we show that a pathogen exploits a resistance protein by activating it to confer susceptibility. Interactions of victorin, an effector produced by the necrotrophic fungus Cochliobolus victoriae, TRX-h5, a defense-associated thioredoxin, and LOV1, an Arabidopsis susceptibility protein, recapitulate the guard mechanism of plant defense. In LOV1's absence, victorin inhibits TRX-h5 resulting in compromised defense but not disease by C. victoriae. In LOV1's presence, victorin binding to TRX-h5 activates LOV1 and elicits a resistance-like response that confers disease susceptibility. We propose that victorin is or mimics a conventional pathogen virulence effector that was defeated by LOV1 and confers virulence to C. victoriae solely because it incites defense.

http://www.sciencemag.org/content/early/2012/10/18/science.1226743.long

批量Blast

批量Blast就是指多个序列的Blast。


blastall -p blastn -d BlastDB -i in_file.fasta  >blast_output

当in_file.fasta里面只有一个序列时，就是单个Blast啊。in_file.fasta也可以放多个Fasta格式的序列，这样子就是批量Blast了。

当然了，麻烦的是批量Blast之后的结果，一个的话我们可以看得了，当批量上千个时，我们不可能一个个看到的。这种小事情Blast早就想到了。这就引进了-m8参数。-b5参数是指显示匹配的前5个结果
blastall -p blastn -d BlastDB -i in_file.fasta  -m8 -b5 >blast_output

 推荐的命令行如下：
blastall -p blastn -d BlastDB -i in_file.fasta  -m8 -b5 -b1 -a2 -FF >blast_output
-a2参数是用二个CPU，加速。-FF是不过滤简单的重复序列和低复杂度的序列（默认是过滤的）。
本文详细出处参考：http://liucheng.name/1221/