Linux command
compseq 命令
文件
复制后可按需替换文件名、目录或参数。
常用示例
Example
compseq [path/to/file.fasta]
Example
compseq [path/to/input_protein.fasta] -word 2 [path/to/output_file.comp]
Example
compseq [path/to/input_dna.fasta] -word 6 [path/to/output_file.comp] -nozero
Example
compseq -sequence [path/to/input_rna.fasta] -word 3 [path/to/output_file.comp] -nozero -frame [1]
Compare
compseq -sequence [path/to/file.fasta] -word 3 [path/to/output.comp] -nozero -infile [path/to/previous.comp]
Example
compseq -sequence [path/to/file.fasta] -word 3 [path/to/output.comp] -nozero -calcfreq
说明
compseq is a bioinformatics tool from the EMBOSS (European Molecular Biology Open Software Suite) package that performs k-mer frequency analysis on DNA, RNA, and protein sequences. It reads sequences in FASTA format and generates compositional statistics showing how often each possible word (k-mer) of a specified length appears in the sequence. The tool is widely used in molecular biology for multiple applications: analyzing codon usage bias in genes, identifying sequence composition patterns that indicate functional or structural elements, and comparing sequence characteristics across organisms or genomic regions. By specifying different word sizes, researchers can examine dinucleotide frequencies (word size 2), codon frequencies (word size 3), or longer oligonucleotide patterns. compseq can calculate both observed frequencies and expected frequencies based on the overall base composition, making it useful for identifying statistically significant deviations from random distribution. The reading frame parameter allows analysis of coding sequences in specific frames, critical for studying codon usage patterns in protein-coding genes.
参数
- -word _size_
- Word size to count (e.g., 2 for dinucleotides, 3 for codons)
- -frame _number_
- Reading frame (1, 2, or 3)
- -nozero
- Ignore zero counts in output
- -infile _file_
- Compare to previous compseq output
- -calcfreq
- Calculate expected frequencies from input
- -help
- Display help
FAQ
What is the compseq command used for?
compseq is a bioinformatics tool from the EMBOSS (European Molecular Biology Open Software Suite) package that performs k-mer frequency analysis on DNA, RNA, and protein sequences. It reads sequences in FASTA format and generates compositional statistics showing how often each possible word (k-mer) of a specified length appears in the sequence. The tool is widely used in molecular biology for multiple applications: analyzing codon usage bias in genes, identifying sequence composition patterns that indicate functional or structural elements, and comparing sequence characteristics across organisms or genomic regions. By specifying different word sizes, researchers can examine dinucleotide frequencies (word size 2), codon frequencies (word size 3), or longer oligonucleotide patterns. compseq can calculate both observed frequencies and expected frequencies based on the overall base composition, making it useful for identifying statistically significant deviations from random distribution. The reading frame parameter allows analysis of coding sequences in specific frames, critical for studying codon usage patterns in protein-coding genes.
How do I run a basic compseq example?
Run `compseq [path/to/file.fasta]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -word _size_ do in compseq?
Word size to count (e.g., 2 for dinucleotides, 3 for codons)