blast常用命令

-dtype: protein: prot;nucleid: nucl

2 step: blastn -query $query -out $outname -db $database_name -evalue 1e-5

blastp -query $query -out $outname -db $database_name (-e e-5)

* blastp -query *.fasta -out *txt -db $database_name -e e-5 -max_target_seqs 3 -outfmt "7 sacc"

3 举例：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"

blastn:这个不用说了吧，核酸对核酸的比对

-db: 指定blast搜索用的数据库，详见上篇文章

-query:用来查询的输入序列，fasta格式

-out：输出结果文件

-evalue: 设置e值cutoff

-max_target_seqs:设置最多的目标序列匹配数（以前我都用-b 5 -v 5,理解不对请指教）

-num_threads：指定多少个cpu运行任务（依赖于你的系统，同于以前的-a参数）

-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，其他可用的特征（红色字体）如下：

*** Formatting options

-outfmt

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

Options 6, 7, and 10 can be additionally configured to produce

a custom format specified by space delimited format specifiers.

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 Qu

ery and subject frames separated by a '/'

qframe means Query frame

sframe means Subject frame

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'