Explanation of options:
Option 1: Allows you to set minimum composition thresholds for your amino acids of interest to identify LCDs that exceed these thresholds.
For example, to search for Q-rich LCDs, you might decide that the LCDs must be at least 50% Q.
You can also choose multiple amino acids with different minimum composition threshold, or group amino acids that should be treated equivalently in the LCD search.
Option 2: Copy and paste your favorite LCD sequence to search for other LCDs with similar compositional features.
LCD-Composer then calculates the most prominent compositional features that define your LCD and automatically converts them to search criteria to look for similar LCDs.
You can choose to incorporate up to 4 features.
Option 3: Search for LCDs within a single protein sequence. This is particularly useful when you would like to define
"multi-faceted" LCDs (i.e. LCDs enriched in multiple amino acids to differing degrees, or when grouping amino acids) within a protein of interest.
This option can also generate customizable, publication-quality plots of amino acid composition as a function of position in your protein.
Option 4: Test for enrichment of LCDs within your protein set of interest. This allows you to define LCD search parameters, search for LCDs
within your proteins of interest and a chosen proteome, and performs a statistical test to see if that type of LCD is enriched (or depleted) within
your protein set of interest. For example, if you believe that Q-rich LCDs are unusually common within your set of transcription factors, you
can search for Q-rich LCDs and automatically perform the enrichment test. This option also contains a built-in "auto-detect" mode, which
will automatically search for the 20 primary classes of LCDs (e.g. A-rich LCDs, C-rich LCDs, D-rich LCDs, etc.), calculates the
degree of enrichment or depletion within your protein set, and generates a publication-quality plot of these results.
Option 5: Identify proteins that contain two distinct types of LCDs ("co-occurring" LCDs). Previously, we found that proteins containing
two different types of LCDs are sometimes associated with very specific functions (Cascarina et al. (2021)).
This option allows you to compare two different LCD-Composer search results files to identify only proteins that appear in both sets.
For example, if you search for positively charged LCDs (H/K/R-rich LCDs) and negatively charged LCDs (D/E-rich LCDs), you
may wish to know which proteins then contain both types of LCDs.
Additionally, the LCD boundaries for each protein are compared so that you will also know whether the LCDs are spatially overlapping or entirely distinct within the sequence.
The results of these comparisons are then returned to you as a new results file containing only the proteins with both types of LCDs.
This can be performed for a maximum of 3 types of LCDs.
Integrated GO-term Analysis: Options 1, 2, and 4 offer automated GO-term analysis of your protein sets using the GOATOOLS Python package.
This allows you to test whether any functional annotations are significantly enriched or depleted among your set of proteins.
If you use GO-term analyses generated by the LCD-Composer webserver in a publication, please cite the following reference (Klopfenstein et al. (2018)).
