compseq

Calculate the composition of unique words in sequences. tldr-pages

On Linux

Linux

from tldr-pages, CC BY 4.0

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

compseq path/to/file.fastaIdentify

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.compIdentify

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 -nozeroIdentify

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 1Identify

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 3Identify

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

Identify

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 -calcfreqIdentify

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

compseq -helpIdentify