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. If you run multiple LCD searches on the same set of proteins, it is up to you as the user to apply an appropriate multiple-hypothesis test correction when applicable. View the "HELP" tab for further guidance. Input a list of UniProt protein identifiers (one per line): Corresponding organism: Homo sapiens (Human) - UP000005640_9606 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) - UP000002311_559292 Mus musculus (Mouse) - UP000000589_10090 Rattus norvegicus (Rat) - UP000002494_10116 Drosophila melanogaster (Fruit fly) - UP000000803_7227 Caenorhabditis elegans - UP000001940_6239 Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2) - UP000464024_2697049 Escherichia coli (strain K12) - UP000000625_83333 Arabidopsis thaliana (Mouse-ear cress) - UP000006548_3702 Danio rerio (Zebrafish) (Brachydanio rerio) - UP000000437_7955 Dictyostelium discoideum (Slime mold) - UP000002195_44689 Xenopus laevis (African clawed frog) - UP000186698_8355 Gallus gallus (Chicken) - UP000000539_9031 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) - UP000002485_284812 Canis lupus familiaris (Dog) (Canis familiaris) - UP000002254_9615 Heterocephalus glaber (Naked mole rat) - UP000006813_10181 Macaca mulatta (Rhesus macaque) - UP000006718_9544 Zea mays (Maize) - UP000007305_4577 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) - UP000008143_8364 Chlamydomonas reinhardtii (Chlamydomonas smithii) - UP000006906_3055 Cavia porcellus (Guinea pig) - UP000005447_10141 Bacillus subtilis (strain 168) - UP000001570_224308 Aliivibrio fischeri (strain ATCC 700601 / ES114) (Vibrio fischeri) - UP000000537_312309 Amphimedon queenslandica (Sponge) - UP000007879_400682 Anolis carolinensis (Green anole) (American chameleon) - UP000001646_28377 Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (Yeast) (Eremothecium gossypii) - UP000000591_284811 Astyanax mexicanus (Blind cave fish) (Astyanax fasciatus mexicanus) - UP000018467_7994 Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) - UP000001414_226186 Brachypodium distachyon (Purple false brome) (Trachynia distachya) - UP000008810_15368 Branchiostoma floridae (Florida lancelet) (Amphioxus) - UP000001554_7739 Callosobruchus maculatus (Southern cowpea weevil) (Pulse bruchid) - UP000410492_64391 Ciona intestinalis (Transparent sea squirt) (Ascidia intestinalis) - UP000008144_7719 Columba livia (Rock dove) - UP000053872_8932 Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) (Filobasidiella neoformans) - UP000002149_214684 Daphnia magna - UP000076858_35525 Emiliania huxleyi (Pontosphaera huxleyi) - UP000013827_2903 Gasterosteus aculeatus (Three-spined stickleback) - UP000007635_69293 Gryllus bimaculatus nudivirus - UP000203733_432587 Macrostomum lignano - UP000215902_282301 Marchantia polymorpha (Liverwort) (Marchantia aquatica) - UP000244005_3197 Marchantia polymorpha subsp. ruderalis - UP000077202_1480154 Medicago truncatula (Barrel medic) (Medicago tribuloides) - UP000002051_3880 Mesocricetus auratus (Golden hamster) - UP000189706_10036 Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) - UP000000807_243273 Myotis lucifugus (Little brown bat) - UP000001074_59463 Naegleria gruberi (Amoeba) - UP000006671_5762 Nematostella vectensis (Starlet sea anemone) - UP000001593_45351 Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) - UP000001805_367110 Nicotiana tabacum (Common tobacco) - UP000084051_4097 Oikopleura dioica (Tunicate) - UP000001307_34765 Oryza sativa subsp. indica (Rice) - UP000007015_39946 Oryza sativa subsp. japonica (Rice) - UP000059680_39947 Oryzias latipes (Japanese rice fish) (Japanese killifish) - UP000001038_8090 Petromyzon marinus (Sea lamprey) - UP000245300_7757 Physcomitrella patens subsp. patens (Moss) - UP000006727_3218 Poecilia reticulata (Guppy) (Acanthophacelus reticulatus) - UP000242638_8081 Populus trichocarpa (Western balsam poplar) (Populus balsamifera subsp. trichocarpa) - UP000006729_3694 Pristionchus pacificus (Parasitic nematode) - UP000005239_54126 Pseudomonas fluorescens (strain F113) - UP000005437_1114970 Schizophyllum commune (strain H4-8 / FGSC 9210) (Split gill fungus) - UP000007431_578458 Selaginella moellendorffii (Spikemoss) - UP000001514_88036 Setaria viridis (Green bristlegrass) (Setaria italica subsp. viridis) - UP000298652_4556 Stentor coeruleus - UP000187209_5963 Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) - UP000001973_100226 Strongylocentrotus purpuratus (Purple sea urchin) - UP000007110_7668 Synechocystis sp. (strain PCC 6803 / Kazusa) - UP000001425_1111708 Taeniopygia guttata (Zebra finch) (Poephila guttata) - UP000007754_59729 Takifugu rubripes (Japanese pufferfish) (Fugu rubripes) - UP000005226_31033 Tetrahymena thermophila (strain SB210) - UP000009168_312017 Thalassiosira pseudonana (Marine diatom) (Cyclotella nana) - UP000001449_35128 Tribolium castaneum (Red flour beetle) - UP000007266_7070 Trichoplax adhaerens (Trichoplax reptans) - UP000009022_10228 Ustilago maydis (strain 521 / FGSC 9021) (Corn smut fungus) - UP000000561_237631 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. NOTE: please think carefully about how isoforms may affect the statistics. If your protein set theoretically could contain all isoforms for an organism, then it is recommended that you check this box. If your protein set only contains one representative sequence per protein, then it is recommended that you do not check this box. Including all isoforms may skew LCD frequency/enrichment statistics. For additional guidance, please visit the "HELP" tab. Run auto-detect mode?: By default, this mode will simultaneously test for enrichment of simple LCDs from every simple LCD class (e.g. A-rich LCDs, C-rich LCDs, D-rich LCDs, etc.). Simple LCDs are defined as LCDs with greater than or equal to 40% composition corresponding to a single amino acid. This mode is useful for exploratory analysis in the absence of a specific hypothesis regarding which types of LCDs may be enriched in your protein set. NOTE: running all statistical tests simultaneously is great for exploratory analyses but reduces your statistical power since a multiple-hypothesis test correction is applied. If you have a pre-conceived hypothesis that a specific type of LCD is enriched in your protein set, then the "auto-detect" method is not recommended. Instead, uncheck this box and use the custom search parameters to test for specific enrichment of your LCD type.
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.