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+# 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 normalised 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`