用blast blastn进行短序列的搜索（比对）

blastn 多加上  -task blastn-short -word_size 7 -evalue 1

-task：设置比对模式，通常情况会有一个默认task，这里要设置为blastn-short
-word_size：尽可能小，这里设为7
-evalue：类似于p值的一个指标，越小说明越可靠

 

Tasks

Task	Description
blastp	Traditional BLASTP to compare a protein query to a protein database
blastp-short	BLASTP optimized for queries shorter than 30 residues
blastn	Traditional BLASTN requiring an exact match of 11
blastn-short	BLASTN program optimized for sequences shorter than 50 bases
megablast	Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences
dc-megablast	Discontiguous megablast used to find more distant (e.g., interspecies) sequences

 

REF

http://barcwiki.wi.mit.edu/wiki/blastTips

https://web.cas.org/help/BLAST/topics/shrt_seq.htm

https://www.jianshu.com/p/a6ee3d19b832?utm_campaign=maleskine