compseq

Calculate the composition of unique words in sequences.

TLDR

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