compseq Command Examples

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