用blast blastn進行短序列的搜索(比對)


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

-task:設置比對模式,通常情況會有一個默認task,這里要設置為blastn-short
-word_size:盡可能小,這里設為7
-evalue:類似於p值的一個指標,越小說明越可靠

 

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


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