mirror of https://github.com/CrimsonTome/tldr.git
37 lines
1.8 KiB
Markdown
37 lines
1.8 KiB
Markdown
|
# 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`
|