Linux command
tblastx 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 query against database
tblastx -query [sequence.fasta] -db [database] -out [results.txt]
Search with specific output format
tblastx -query [sequence.fasta] -db [database] -outfmt [6]
Search against local FASTA file
tblastx -query [query.fasta] -subject [subject.fasta]
Set e-value threshold
tblastx -query [sequence.fasta] -db [database] -evalue [1e-5]
Use multiple threads
tblastx -query [sequence.fasta] -db [database] -num_threads [4]
Limit number of alignments
tblastx -query [sequence.fasta] -db [database] -max_target_seqs [10]
Display help
tblastx -help
说明
tblastx searches a translated nucleotide query against a translated nucleotide database. Both query and database sequences are translated in all six reading frames (three forward, three reverse), and protein-level comparisons are performed. This program is useful for finding distant protein-coding relationships between nucleotide sequences, especially when working with unannotated genomic or EST data. It is computationally intensive due to the multiple translations. Unlike other BLAST programs, tblastx only supports ungapped alignments. For sequences with insertions or deletions, consider using blastx or tblastn instead. Part of the NCBI BLAST+ suite, tblastx requires properly formatted BLAST databases created with makeblastdb.
参数
- -query _file_
- Input FASTA file with nucleotide query sequence(s).
- -db _database_
- BLAST database name to search.
- -subject _file_
- Subject sequence file for pairwise comparison.
- -out _file_
- Output file (default: stdout).
- -outfmt _format_
- Output format (0=pairwise, 6=tabular, 7=tabular with comments, etc.).
- -evalue _value_
- Expectation value threshold (default: 10).
- -max_target_seqs _n_
- Maximum number of aligned sequences to keep.
- -num_threads _n_
- Number of CPU threads to use.
- -query_gencode _code_
- Genetic code for query translation.
- -db_gencode _code_
- Genetic code for database translation.
- -strand _strand_
- Query strand(s) to search: both, plus, minus.
- -soft_masking _bool_
- Apply soft masking to query.
- -seg _value_
- Filter query with SEG (yes, no, or parameters).
- -matrix _name_
- Scoring matrix (default: BLOSUM62).
- -word_size _n_
- Word size for initial match.
- -h, -help
- Display help information.
FAQ
What is the tblastx command used for?
tblastx searches a translated nucleotide query against a translated nucleotide database. Both query and database sequences are translated in all six reading frames (three forward, three reverse), and protein-level comparisons are performed. This program is useful for finding distant protein-coding relationships between nucleotide sequences, especially when working with unannotated genomic or EST data. It is computationally intensive due to the multiple translations. Unlike other BLAST programs, tblastx only supports ungapped alignments. For sequences with insertions or deletions, consider using blastx or tblastn instead. Part of the NCBI BLAST+ suite, tblastx requires properly formatted BLAST databases created with makeblastdb.
How do I run a basic tblastx example?
Run `tblastx -query [sequence.fasta] -db [database] -out [results.txt]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -query _file_ do in tblastx?
Input FASTA file with nucleotide query sequence(s).