转载：http://blog.sina.com.cn/s/blog_5ecfd9d90100ksui.html
http://www.docin.com/p-704735699.html
与之前的blast相比，新的blast+将blastn,blastx等合作与blastall命令分隔开来，对各个命令的参数定制更加方便个人在使用blastn的过程中总结了一些自认为常用的参数。
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: 用来查询的输入序列，fasta格式
-db: 指定blast搜索用的数据库，详见上篇文章
-out： 输出结果文件
-evalue: 设置e值cutoff
-outfmt format "7 qacc sacc evalue length pident" ：这个是新BLAST+中最拉风的功能了，直接控制输出格式，不用再用parser啦。 7表示带注释行的tab格式的输出，可以自定 义要输出哪些内容，用空格分格跟在7的后面，并把所有的输出控制用双引号括起来，其中qacc查询序列的 acc,sacc表示目标序列的acc，evalue即是e值，length即是匹配的长 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‘