Linux command
tblastn 命令
文本
复制后可按需替换文件名、目录或参数。
常用示例
Search a protein query
tblastn -query [protein.fasta] -db [nt_database]
Search with a specific output format
tblastn -query [protein.fasta] -db [database] -outfmt [6]
Save results to a file
tblastn -query [protein.fasta] -db [database] -out [results.txt]
Use multiple threads
tblastn -query [protein.fasta] -db [database] -num_threads [4]
Set E-value threshold
tblastn -query [protein.fasta] -db [database] -evalue [1e-10]
Use the fast task
tblastn -query [protein.fasta] -db [database] -task tblastn-fast
Search against a remote NCBI database
tblastn -query [protein.fasta] -db [nr] -remote
说明
tblastn is part of the NCBI BLAST+ suite for sequence alignment. It searches a protein query sequence against a nucleotide sequence database, translating the database sequences in all six reading frames at search time. This is useful for finding protein-coding regions in nucleotide sequences. The algorithm compares each protein query against the translated nucleotide subjects and reports statistically significant alignments. Results can be formatted in various ways for downstream analysis, including tabular formats suitable for parsing.
参数
- -query _file_
- Input file with protein query sequence(s) in FASTA format.
- -db _database_
- Nucleotide database name or path to search against.
- -out _file_
- Output file for results (default: stdout).
- -outfmt _format_
- Output format: 0 (pairwise), 6 (tabular), 7 (tabular with comments), 10 (CSV), and others.
- -evalue _value_
- E-value threshold for reporting matches (default: 10).
- -num_threads _n_
- Number of threads for parallel execution.
- -task _task_
- Task to execute: tblastn (standard) or tblastn-fast (faster, larger word size).
- -remote
- Execute search against NCBI servers instead of local database.
- -max_target_seqs _n_
- Maximum number of aligned sequences to keep.
- -word_size _n_
- Word size for initial match (default: 3 for tblastn, 6 for tblastn-fast).
- -matrix _name_
- Scoring matrix (default: BLOSUM62). Other options include PAM30, PAM70, BLOSUM45, BLOSUM80.
- -gapopen _n_
- Cost to open a gap.
- -gapextend _n_
- Cost to extend a gap.
- -db_gencode _n_
- Genetic code to translate database sequences (default: 1).
- -comp_based_stats _mode_
- Composition-based statistics mode (0-3).
- -seg _options_
- Filter query with SEG algorithm.
- -threshold _n_
- Minimum score to add a word to the BLAST lookup table (default: 13 for tblastn, 21 for tblastn-fast).
- -h
- Print abbreviated help.
- -help
- Print detailed help with all options.
- -version
- Print version information.
FAQ
What is the tblastn command used for?
tblastn is part of the NCBI BLAST+ suite for sequence alignment. It searches a protein query sequence against a nucleotide sequence database, translating the database sequences in all six reading frames at search time. This is useful for finding protein-coding regions in nucleotide sequences. The algorithm compares each protein query against the translated nucleotide subjects and reports statistically significant alignments. Results can be formatted in various ways for downstream analysis, including tabular formats suitable for parsing.
How do I run a basic tblastn example?
Run `tblastn -query [protein.fasta] -db [nt_database]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -query _file_ do in tblastn?
Input file with protein query sequence(s) in FASTA format.