Linux command
blastn 命令
文本
复制后可按需替换文件名、目录或参数。
常用示例
Align sequences
blastn -query [query.fa] -subject [subject.fa] -evalue [1e-9]
Example
blastn -task blastn -query [query.fa] -subject [subject.fa]
Example
blastn -query [query.fa] -subject [subject.fa] -outfmt '6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident' -out [output.tsv]
Example
blastn -query [query.fa] -db [path/to/blast_db] -num_threads [16] -max_target_seqs [10]
Example
blastn -query [query.fa] -db nt -remote
Example
blastn -h
说明
blastn performs nucleotide-to-nucleotide BLAST (Basic Local Alignment Search Tool) searches. It finds regions of similarity between nucleotide sequences, which can indicate functional, structural, or evolutionary relationships. The tool supports multiple search algorithms including megablast (default, for highly similar sequences), discontiguous megablast, and standard blastn. Results can help identify genes, compare genomes, or find homologous sequences.
参数
- -query _file_
- Input file with query sequences in FASTA format
- -subject _file_
- Subject sequence file for direct comparison
- -db _name_
- BLAST database name for searching
- -evalue _threshold_
- Expectation value (E) threshold for reporting matches
- -task _name_
- Algorithm variant: megablast, dc-megablast, or blastn
- -outfmt _format_
- Output format (0=pairwise, 6=tabular, 7=tabular with headers)
- -out _file_
- Output file name
- -num_threads _n_
- Number of CPU threads to use
- -max_target_seqs _n_
- Maximum number of aligned sequences to keep
- -remote
- Execute search on NCBI servers
FAQ
What is the blastn command used for?
blastn performs nucleotide-to-nucleotide BLAST (Basic Local Alignment Search Tool) searches. It finds regions of similarity between nucleotide sequences, which can indicate functional, structural, or evolutionary relationships. The tool supports multiple search algorithms including megablast (default, for highly similar sequences), discontiguous megablast, and standard blastn. Results can help identify genes, compare genomes, or find homologous sequences.
How do I run a basic blastn example?
Run `blastn -query [query.fa] -subject [subject.fa] -evalue [1e-9]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -query _file_ do in blastn?
Input file with query sequences in FASTA format