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


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