Supporting online material
for:
CHOP proteins into structural domain-like fragments

Jinfeng Liu ^1,3,4,*, & Burkhard Rost ^1,2,3,*

TOC for Supplement:

Fig. S1: CHOP was robust with respect to parameter choices. The two major free parameters for CHOP are (1) the required coverage of a domain annotated by PrISM or Pfam-A (values from 0.7-0.9, i.e. 70-90% of the annotated domain have to be sequence similar), and (2) the required threshold for sequence similarity (shown BLAST E-values from 0.1-0.001, i.e. matches are accepted if more similar than this threshold). The data shown was compiled for the yeast proteome. The maximum number (14,047) was obtained at coverage of 80% and E-value of 0.1 (right dashed line), the minimum was 13,915 (left dashed line). For the parameters we used (coverage of 80% and E-value of 0.01, central solid line), the number was 13,988. Thus, the variations in the results for CHOP between throughout this extensive parameter range were smaller than 1%.

Fig. S2: PrISM and Pfam-A predicted similar number of domains for same proteins. 6,349 yeast proteins were chopped according to PrISM alone or Pfam-A alone and compared for the number of predicted domains. 1,521 of them can be dissected by either of them. In 40% of the cases, predictions from PrISM and Pfam are the same. Cumulatively, the difference is smaller than three domains for 90% of the proteins.

Fig. S3: Percentage of single domain proteins in proteomes. As expected, eukaryotic proteomes (blue) have more multi-domain proteins, than do prokaryotes (green) and archae bacteria (red).

Fig. S4: CLUP versus other family-based databases. The distribution of CLUP lengths was most similar to that of the semi-automatic domain parsing method SBase: both slightly over-represented regions ²50 residues, and over-represented (with respect to SCOP) fragments with over 360 residues. Both also came closest to Pfam-A regions. For all public methods the results are taken from the respective databases.

Table S1: Names and numbers of ORFs for 62 proteomes used