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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