Linux command
blastx 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 translated nucleotide
blastx -query [sequences.fasta] -db [nr] -out [results.txt]
Output in tabular format
blastx -query [sequences.fasta] -db [swissprot] -outfmt 6 -out [results.tsv]
Output in XML format
blastx -query [sequences.fasta] -db [nr] -outfmt 5 -out [results.xml]
Set E-value threshold
blastx -query [sequences.fasta] -db [nr] -evalue [0.001] -out [results.txt]
Limit number of alignments
blastx -query [sequences.fasta] -db [nr] -max_target_seqs [10] -out [results.txt]
Use multiple threads
blastx -query [sequences.fasta] -db [nr] -num_threads [8] -out [results.txt]
Show help
blastx -help
说明
blastx translates a nucleotide query sequence in all six reading frames and searches it against a protein database. It is part of the NCBI BLAST+ suite for sequence similarity searching. This tool is useful for identifying protein homologs of nucleotide sequences, annotating genes, and finding coding regions in DNA sequences.
参数
- -query _file_
- Input nucleotide sequence file (FASTA format)
- -db _name_
- Protein database to search against (e.g., nr, swissprot)
- -out _file_
- Output file for results
- -outfmt _format_
- Output format: 0=pairwise, 5=XML, 6=tabular, 7=tabular with comments
- -evalue _value_
- E-value threshold for reporting hits (default: 10)
- -max_target_seqs _n_
- Maximum number of aligned sequences to keep
- -num_threads _n_
- Number of threads/CPUs to use
- -word_size _n_
- Word size for initial match
- -matrix _name_
- Scoring matrix (e.g., BLOSUM62, PAM250)
- -query_gencode _n_
- Genetic code for query translation (default: 1).
- -seg _method_
- Filter query sequence for low-complexity regions (default: 12 2.2 2.5).
- -task _name_
- Task to execute: blastx (default) or blastx-fast.
- -remote
- Execute search remotely on NCBI servers.
FAQ
What is the blastx command used for?
blastx translates a nucleotide query sequence in all six reading frames and searches it against a protein database. It is part of the NCBI BLAST+ suite for sequence similarity searching. This tool is useful for identifying protein homologs of nucleotide sequences, annotating genes, and finding coding regions in DNA sequences.
How do I run a basic blastx example?
Run `blastx -query [sequences.fasta] -db [nr] -out [results.txt]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -query _file_ do in blastx?
Input nucleotide sequence file (FASTA format)