Linux command
blastdbcmd 命令
文本
复制后可按需替换文件名、目录或参数。
常用示例
Get database information
blastdbcmd -db [nr] -info
List available databases
blastdbcmd -list [/path/to/databases] -recursive
Extract a sequence
blastdbcmd -db [nr] -entry [NP_001234] -out [sequence.fasta]
Extract all sequences
blastdbcmd -db [swissprot] -entry all -out [swissprot.fasta]
Extract sequences
blastdbcmd -db [nr] -entry_batch [ids.txt] -out [sequences.fasta]
Get sequence in specific format
blastdbcmd -db [nr] -entry [NP_001234] -outfmt "%a %t %s"
Show BLAST database search path
blastdbcmd -show_blastdb_search_path
Get taxonomy information
blastdbcmd -db [nr] -entry [NP_001234] -outfmt "%a %S %T"
说明
blastdbcmd is a utility for extracting sequences and metadata from BLAST databases. It can retrieve individual sequences by accession, extract all sequences, display database statistics, and generate custom reports. The tool is part of the NCBI BLAST+ suite and works with databases created by makeblastdb or downloaded from NCBI.
参数
- -db _name_
- BLAST database name or path
- -entry _id_
- Sequence identifier(s) to retrieve; use "all" for entire database
- -entry_batch _file_
- File containing list of sequence identifiers
- -out _file_
- Output file (default: stdout).
- -outfmt _format_
- Custom output format string using % tokens.
- -info
- Display database information (type, number of sequences, total length, date).
- -list _path_
- List databases in specified path.
- -recursive
- Search directories recursively (with -list).
- -show_blastdb_search_path
- Display BLAST database search paths.
- -dbtype _type_
- Database type: nucl (nucleotide) or prot (protein). Needed when both types share a name.
- -target_only
- Retrieve only target sequences (no redundant group members).
- -tax_info
- Display taxonomy information (requires taxonomy database).
- -range _start-stop_
- Extract subsequence range (1-based, inclusive).
- -strand _strand_
- Strand to retrieve: plus or minus (nucleotide only).
- -line_length _N_
- Line length for FASTA output (default: 80). Use 0 for single-line sequences.
- -long_seqids
- Use long sequence identifiers including database and accession.version.
FAQ
What is the blastdbcmd command used for?
blastdbcmd is a utility for extracting sequences and metadata from BLAST databases. It can retrieve individual sequences by accession, extract all sequences, display database statistics, and generate custom reports. The tool is part of the NCBI BLAST+ suite and works with databases created by makeblastdb or downloaded from NCBI.
How do I run a basic blastdbcmd example?
Run `blastdbcmd -db [nr] -info` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -db _name_ do in blastdbcmd?
BLAST database name or path