For a detailed description of the parameters, click on the HELP tab above. For more information, you can also refer to the LCD-Composer webserver paper, the original LCD-Composer paper, or the LCD-Composer Github page.

Organism to search for LCDs: If your organism does not appear in the dropdown menu, try submitting the scientific name of your organism (e.g. "Homo sapiens"). A full list of supported organsisms can be downloaded here, and you can copy/paste the scientific name of your favorite organism.

Include all isoforms in the LCD search?: By default, LCD-Composer will only search the UniProt proteome file that contains one representative protein sequence per gene.

Window Size: Default = 20aa. This is scanning window size used by LCD-Composer.

Amino acid(s) of interest: This parameter is the amino acid (e.g. "Q") or groups of amino acids (e.g. "QN_FWY") that you want to use to define LCDs.
Amino acid(s) should ONLY be specified using their single-letter abbreviations, with underscores (_) separating groups when applicable.

Composition threshold(s): Default = 40 (percent). This is the minimum composition threshold for LCDs you want to identify (must be a number between 1-100, inclusive).

Linear dispersion threshold(s): Default = 0.5. This is the minimum linear dispersion of your amino acid(s) of interest in order to be recognized as an LCD.

Linear dispersion method: New method Original method Default = New method. The new method allows you to set a separate linear dispersion threshold for each group of amino acids. The original method uses a single linear dispersion threshold for all amino acid groups combined (this is the original behavior of the LCD-Composer algorithm).

Threshold to ignore dispersion: Default = halfway between your composition threshold and 100. This is the composition threshold at which LCD-Composer ignores the linear dispersion criterium.
It is recommended that you leave this box blank, which will use the default in LCD-Composer.

Run a GO-term analysis on resulting LCD-containing proteins?: By default, GO-term analysis is not performed. GO-term analysis is only available for select organisms (see "HELP" page for more details). It is recommended that you only run a GO-term analysis once you have finalized your decision on the best LCD search parameters for your hypothesis/application. Otherwise, you may need to consider additional measures for correcting p-values (see "HELP" page).