轉載：http://blog.sina.com.cn/s/blog_5ecfd9d90100ksui.html
http://www.docin.com/p-704735699.html
與之前的blast相比，新的blast+將blastn,blastx等合作與blastall命令分隔開來，對各個命令的參數定制更加方便個人在使用blastn的過程中總結了一些自認為常用的參數。
1、例子： blastn -db plant_rna -query test.fa -out test.out -evalue 0.00001 -max_target_seqs 5 -num_threads 4 -outfmt format "7 qacc sacc evalue length pident"
-query: 用來查詢的輸入序列，fasta格式
-db: 指定blast搜索用的數據庫，詳見上篇文章
-out： 輸出結果文件
-evalue: 設置e值cutoff
-outfmt format "7 qacc sacc evalue length pident" ：這個是新BLAST+中最拉風的功能了，直接控制輸出格式，不用再用parser啦。 7表示帶注釋行的tab格式的輸出，可以自定 義要輸出哪些內容，用空格分格跟在7的后面，並把所有的輸出控制用雙引號括起來，其中qacc查詢序列的 acc,sacc表示目標序列的acc，evalue即是e值，length即是匹配的長 度，pident即是序列相同的百分比。
2、Formatting options
-outfmt <String>
alignment view options:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = XML Blast output,
6 = tabular,
7 = tabular with comment lines,
8 = Text ASN.1,
9 = Binary ASN.1
10 = Comma-separated values
3、Options 6, 7, and 10 can be additionally configured to producea custom format specified by space delimited format specifiers.
（1）The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
sallacc means All subject accessions
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
（2）When not provided, the default value is:
'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore', which is equivalent to the keyword 'std'
Default = ’0‘