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compseq — Calculate the composition of unique words in sequences. More information: <https://www.bioinformatic

Submitted by: @import:tldr-pages·Mar 2, 2026·

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compseqthecommandcliwordscompositionuniquecalculate

linux

Problem

How to use the compseq command: Calculate the composition of unique words in sequences. More information: <https://www.bioinformatics.nl/cgi-bin/emboss/help/compseq/>.

Solution

compseq — Calculate the composition of unique words in sequences. More information: <https://www.bioinformatics.nl/cgi-bin/emboss/help/compseq/>.

Count observed frequencies of words in a FASTA file, providing parameter values with interactive prompt:

compseq {{path/to/file.fasta}}

Count observed frequencies of amino acid pairs from a FASTA file, save output to a text file:

compseq {{path/to/input_protein.fasta}} -word 2 {{path/to/output_file.comp}}

Count observed frequencies of hexanucleotides from a FASTA file, save output to a text file and ignore zero counts:

compseq {{path/to/input_dna.fasta}} -word 6 {{path/to/output_file.comp}} -nozero

Count observed frequencies of codons in a particular reading frame; ignoring any overlapping counts (i.e. move window across by word-length 3):

compseq -sequence {{path/to/input_rna.fasta}} -word 3 {{path/to/output_file.comp}} -nozero -frame {{1}}

Count observed frequencies of codons frame-shifted by 3 positions; ignoring any overlapping counts (should report all codons except the first one):

compseq -sequence {{path/to/input_rna.fasta}} -word 3 {{path/to/output_file.comp}} -nozero -frame 3

Count amino acid triplets in a FASTA file and compare to a previous run of compseq to calculate expected and normalized frequency values:

compseq -sequence {{path/to/human_proteome.fasta}} -word 3 {{path/to/output_file1.comp}} -nozero -infile {{path/to/output_file2.comp}}

Approximate the above command without a previously prepared file, by calculating expected frequencies using the single base/residue frequencies in the supplied input sequence(s):

compseq -sequence {{path/to/human_proteome.fasta}} -word 3 {{path/to/output_file.comp}} -nozero -calcfreq

Display help (use -help -verbose for more information on associated and general qualifiers):

compseq -help

Code Snippets

Count observed frequencies of words in a FASTA file, providing parameter values with interactive prompt

compseq {{path/to/file.fasta}}

Count observed frequencies of amino acid pairs from a FASTA file, save output to a text file

compseq {{path/to/input_protein.fasta}} -word 2 {{path/to/output_file.comp}}

Count observed frequencies of hexanucleotides from a FASTA file, save output to a text file and ignore zero counts

compseq {{path/to/input_dna.fasta}} -word 6 {{path/to/output_file.comp}} -nozero

Count observed frequencies of codons in a particular reading frame; ignoring any overlapping counts (i.e. move window across by word-length 3)

compseq -sequence {{path/to/input_rna.fasta}} -word 3 {{path/to/output_file.comp}} -nozero -frame {{1}}

Count observed frequencies of codons frame-shifted by 3 positions; ignoring any overlapping counts (should report all codons except the first one)

compseq -sequence {{path/to/input_rna.fasta}} -word 3 {{path/to/output_file.comp}} -nozero -frame 3

Context

tldr-pages: linux/compseq

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