blastn 输出结果每列啥意思_blast使用和输出

一、建立索引

formatdb -i ref.fna -p F -n ref.fna

-p: T=protein

F=nucleotide

default = T

-n:重命名数据库文件的名称

二、比对

blastn

blastall -p blastn -i query.fa -d ref.fna -e 1e-06 -m 8 -o output.fmt8.txt

-m:输出格式

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 = query-anchored no identities and blunt ends,

6 = flat query-anchored, no identities and blunt ends,

7 = XML Blast output,

8 = tabular,

9 tabular with comment lines

10 ASN, text

11 ASN, binary [Integer]

fmt=8：

0

1

2

3

4

5

6

7

8

9

10

11

qseqid

sseqid

pident

length

mismatch

gapopen

qstart

qend

sstart

send

evalue

bitscore

自定义格式：

-outfmt "8 qseqid sseqid evalue"

column 1

column 2

qseqid

Query Seq-id

qgi

Query GI

qacc

Query accesion

qaccver

Query accesion.version

qlen

Query sequence length

sseqid

Subject Seq-id

sallseqid

All subject Seq-id(s), separated by a ';'

sgi

Subject GI

sallgi

All subject GIs

sacc

Subject accession

saccver

Subject accession.version

sallacc

All subject accessions

slen

Subject sequence length

qstart

Start of alignment in query

qend

End of alignment in query

sstart

Start of alignment in subject

send

End of alignment in subject

qseq

Aligned part of query sequence

sseq

Aligned part of subject sequence

evalue

Expect value

bitscore

Bit score

score

Raw score

length

Alignment length

pident

Percentage of identical matches

nident

Number of identical matches

mismatch

Number of mismatches

positive

Number of positive-scoring matches

gapopen

Number of gap openings

gaps

Total number of gaps

ppos

Percentage of positive-scoring matches

frames

Query and subject frames separated by a '/'

qframe

Query frame

sframe

Subject frame

btop

Blast traceback operations (BTOP)

staxids

Subject Taxonomy ID(s), separated by a ';'

sscinames

Subject Scientific Name(s), separated by a ';'

scomnames

Subject Common Name(s), separated by a ';'

sblastnames

Subject Blast Name(s), separated by a ';' (in alphabetical order)

sskingdoms

Subject Super Kingdom(s), separated by a ';' (in alphabetical order)

stitle

Subject Title

salltitles

All Subject Title(s), separated by a '<>'

sstrand

Subject Strand

qcovs

Query Coverage Per Subject

qcovhsp

Query Coverage Per HSP

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